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They were important years in which both countries pursued policies of growth, often feeding off the energy, access and cooperation that they provided each other. Much of it was a result of Mr Suharto's pragmatic understanding of the benefits of having close and strong ties with neighbours.
Mr Suharto's rule and, in particular, his focus on economic development and improving the livelihood and environment for millions of Indonesians set the course for his country - and the region, allowing nations like Singapore to grow and prosper in a peaceful and stable environment.
As an Asean founding member in 1967 and the grouping's largest member, Indonesia set the tone.
Mr Suharto gave the assurance that Indonesia did not harbour expansionist ambitions, promoted constructive and cooperative relationships to face common problems, and brought countries like Singapore into closer contact with an economic giant in the making.
As Prime Minister Lee Hsien Loong noted on one of his early visits to Indonesia in 1990, much of how bilateral and regional relations developed had a great deal to do with the character and outlook of Mr Suharto.
Also key to the good bilateral ties was the friendship that developed between the Indonesian president and then-prime minister Lee Kuan Yew.
Their close rapport paved the way for relations to develop on the basis of mutual respect and cooperation in a host of areas, from investment and tourism to civil aviation and defence.
According to former Indonesian State Secretary Moerdiono, both leaders also recognised that the kind of linkages being encouraged and developed in the economic realm - cooperation for mutual benefit - formed the basis for ties to transcend personal contacts between political leaders.
His comments had come in an interview ahead of plans to strengthen links in Batam and the wider Riau region through a growth triangle concept involving Singapore, the Indonesian island, and parts of Johor.
Indeed, it was Mr Suharto who had proposed, earlier, in 1976 that Singapore help Indonesia to develop Batam.
A joint venture between a Singapore government-linked company and an Indonesian group set up a Batam industrial park, and cooperation would eventually be expanded to include the neighbouring islands of Bintan and Karimun.
Mr Suharto saw the benefits of linking with a small but dynamic neighbour, not only as a means to strengthen bonds between people, but also because such tie-ups could serve as a catalyst for developing other parts of the country.
It was an era of inter-dependence, he said in 1997 in Karimun.
Jakarta was 'reaping' benefits from its cooperation with Singapore, including a greater inflow of capital, transfer of technology and skills, and greater employment opportunities.
And as he put it candidly, cooperation for Singapore meant the Republic could overcome obstacles it had such as the lack of land, natural and human resources.
Agreements on tourism cooperation, air services, the supply of gas would follow, and served to deepen ties.
By 1998, when Mr Suharto resigned the presidency, Singapore had more than $4 billion of investments in Batam, Bintan, Karimun, Sumatra, Java and elsewhere in Indonesia.
Singapore's banks had another $4 billion in loans to Indonesia.
Singapore was also Indonesia's largest trading partner among the Asean countries, as well as its largest single tourist market, with more than one million visitors a year.
Such links endured through the post-Suharto period, underpinning his view of the need for both sides to have an ongoing relationship that could transcend his time in power.
While investment in the Riau Islands has tapered off in recent years - a result of issues ranging from labour problems to the introduction of regional autonomy that gave local authorities opportunity to impose more levies - both sides are working to woo investors back.
Indonesia under Mr Suharto also did not see Singapore as aggressive or a threat, and had no qualms letting the Singapore military use its territory.
A weapons range near Pekanbaru in Sumatra opened in 1989 for both air forces to use. A 1995 pact gave Singapore's air force more airspace to train in - over the sea in southern Sumatra, and in the north-east near the Natuna islands in the South China Sea.
As political scientist Bilveer Singh noted: 'The relations could reach this far because of the unique, special, front- and back-door relationship of the two men.'
This goodwill was, however, not automatic.
Singapore had seen a threat in Mr Suharto's predecessor Sukarno, who mounted the Konfrontasi campaign in 1963 - a confrontational stance towards the then-Federation of Malaysia, of which Singapore was a part - and practised a coercive diplomacy that came close to war.
All in, 37 bombs hit Singapore. The worst was at MacDonald House along Orchard Road in 1965, which killed three people and injured 33.
Indonesians, in turn, perceived Singapore's majority ethnic Chinese population as a problem. Singapore was seen as a potential supporter - and outpost - of communist China.
It had also been seen as opportunistic as its ports were open to shipments and exports from the archipelago's ethnic Chinese businessmen, and as a means for them to evade domestic taxes and foreign exchange requirements.
But Mr Suharto's de facto military takeover in 1965 ushered in a new era. Feelers were sent out to suss out Singapore's position.
In May 1973, Mr Lee Kuan Yew made a landmark visit to Indonesia that helped set the friendly tone of relations with Mr Suharto.
Throughout the 1970s and 1980s, they met almost every year to keep in touch and discuss matters . Often their meetings were held without advisers or interpreters present.
Observers said both leaders clicked because they were pragmatists who were not afraid to adopt tough policies.
Indonesian political analyst Jusuf Wanandi noted that both shared the same strategy of development: economic development was first, and political stability a prerequisite.
Indonesia under Mr Suharto took the position of a benign power, cooperated with its neighbours and backed the Asean grouping - all of which were in line with Singapore's interests.
Former Singapore ambassador to Indonesia Barry Desker noted that despite leading the group's largest and most-populated country, Mr Suharto was not one to throw his weight around, and gave space to each member to develop in its own way.
'The emergence of Asean as a diplomatic community enjoying strong international recognition and regional support owed much to Indonesian restraint under Suharto's leadership.'
Such developments spelt stability for the region, which in turn made it attractive for foreign investors to sink their funds in South-east Asia, including in Singapore.
Mr Desker recalled instances in which Mr Suharto's enlightened views benefited Singapore.
These included one in 1990, when Singapore offered the use of facilities to American military aircraft and naval vessels as a contribution to the continued US regional presence, following the return of Clark airfield and Subic naval base to the Philippines.
'Mr Suharto's public acceptance of this move quelled criticism from the region,' said Mr Desker.
Singapore also saw in Mr Suharto someone who could be trusted.
He once sought 10,000 tonnes of rice from Singapore for emergency needs because the rice crop had failed, and promised to repay in kind. Indonesia repaid on schedule - and provided rice of even better quality.
MM Lee corroborated this point, recalling in his memoirs: 'As we met over the years, I found him to be a man of his word. He made few promises, but delivered what he had promised. His forte was his consistency.'
While there are those who also say that Mr Suharto's goodwill was not motivated by trust, but by a desire for external parties, such as Singapore, to legitimise his own rule, what is certain is that ties have not been quite the same without him.
Mr Singh notes: 'The relations between the two countries lost this anchor once Suharto fell in May 1998 and bilateral ties have taken a dive ever since, even though there has been some restoration under President Susilo Bambang Yudhoyono - but never to the same scale as it was during the Lee-Suharto period.'
This point can be made in another way.
As MM Lee noted in his memoirs: 'Our bilateral relations over the years from 1965 depended first on getting the measure of each other and learning to co-exist.
'There were always problems to overcome, but we could resolve them, or work around them or set them aside, to be resolved later.
'In retrospect, an Indonesian president with a character and temperament more like Sukarno's would have been difficult to get close to and work with.
'Then the history of this period would have been different for Indonesia, and probably for the whole of South-east Asia.'
