It demonstrates that the 11 nations involved "know how to make a win-win deal" in a time of rising nationalism, protectionism and the threat of trade wars, he added.
PM Lee said in a Facebook post that "it's been a long journey" for the signing of the CPTPP, which was previously known as the TPP or Trans-Pacific Partnership.
It was signed in Santiago, Chile on Thursday afternoon, and is open to new members on top of the existing 11: Australia, Brunei, Canada, Chile, Japan, Malaysia, Mexico, New Zealand, Peru, Singapore and Vietnam.
PM Lee said he was grateful to the other 10 nations for their commitment to the project, which seeks to promote high standards for broader economic integration in the future.
"Japan is the biggest economy in the CPTPP, and Prime Minister Shinzo Abe provided leadership and deftly steered the CPTPP to the finish line," said PM Lee in his Facebook post.
He also thanked Singapore's trade negotiating team, "who slogged for many years, made countless trips and spent much time away from families to make this happen".
Countries will now have to ratify the agreement, a process which involves amending their laws.
"Singapore will ratify the agreement expeditiously, and work closely with our CPTPP partners to improve lives for all our peoples," wrote PM Lee.