Djohar Arifin Husin, a former secretary general of the Indonesian Sports Committee, will be the next chief of PSSI after he defeated the other candidates in two rounds of voting.
The PSSI had been told it must hold elections or face suspension by the game's governing body, which would have jeopardised Indonesia's participation in the second round of 2014 World Cup Asian qualifying later this month.
"There are no sanctions so far for Indonesia. I think the first condition of the congress is in place so we can be rather optimistic," FIFA observer Primo Carvaro, who attended the elections in Solo in central Java, told reporters.
FIFA Executive Committee member Prince Ali bin Al Hussein of Jordan, Asia's vice-president on the executive, welcomed the election result on Saturday.
In a statement from Amman he said: "All Indonesians deserve to see their national team rising to join the champions of Asia and beyond.
"I look forward to visiting Indonesia in the near future to meet with the new PSSI leadership and discuss means of future cooperation to develop football in Indonesia across the board."
Husin polled 61 votes after being backed by supporters of local oil tycoon Arifin Panigoro and army general George Toisutta.
His nearest opponent, Agusman Effendi, got 38 votes and was backed by supporters of former PSSI chairman Nurdin Halid.
Previous elections had failed amid chaotic scenes, and FIFA banned both Panigoro and Toisutta from standing for chairman because of their involvement in launching a breakaway Indonesian League (LPI) that attracted teams from the PSSI-supported Indonesia Super League (ISL).
FIFA appointed a normalisation committee earlier this year to organise the election after opponents of Halid, who was jailed in 2007 for misusing funds but continued to run the PSSI from his cell, forced their way into PSSI elections.
"Now we must focus on moving forward and how to improve in the future, hopefully with support from everyone," said Husin.
Indonesia, ranked 132nd by FIFA, have been drawn to play Turkmenistan in the second round of Asian qualifying, with the first leg to take place on July 23 in Ashgabat before the return in Jakarta five days later.
