Mr Joko, popularly known as Jokowi, is projected to secure 55.7 per cent of votes as shown by Charta Politika's survey conducted from April 5 to April 10.
That compares with a mid-March survey showing he would get 53.5 per cent of ballots cast.
Support for Mr Prabowo is seen at 38.8 per cent from 37.5 per cent earlier, Charta Politika said on Saturday.
As many as 84.2 per cent of respondents said they are sure of their choice when they go to vote on April 17, while 7.2 per cent said they may still change their minds.
The survey of 2,000 respondents in 34 provinces has a margin of error of around 2.19 per cent.
About 5.5 per cent of the respondents said they do not know who they will vote for or did not disclose their support.