The long-running battle over controls of the sport had left the football-obsessed Indonesia country with two leagues and two national teams.
"This is remarkable. It's a major leap for the future of our football," Djohar Arifin Husein, chairman of the Indonesian Football Association (PSSI), said after the PSSI's special congress voted on the issue in a luxury Jakarta hotel.
The meeting was marred by jostling and shouting. Nearly 500 police were on standby at the hotel.
He said the rival Indonesian Soccer Rescue Committee (KPSI),
had agreed to return to the FIFA-recognised PSSI.
"We have one league, one national team, one football federation and we can avoid FIFA's sanction."
FIFA has repeatedly threatened to suspend Indonesia unless it resolved the dispute. Its latest hearing on the issue was due later this month.
The majority of the 100 votes at the meeting agreed to unite the two leagues - the Indonesian Super League (ISL) and Indonesian Premier League (IPL), by 2014 with 18 clubs from ISL and four clubs from IPL.
KPSI chairman La Nyalla Mattaliti was appointed vice chairman of the PSSI. Mattaliti and three other former members of PSSI's governing executive committee were also reappointed.
However, six of the 11 current committee members walked out of the meeting in protest.
Mattaliti told reporters that the six members have been suspended until the next congress in six weeks time when PSSI will elect a new executive committee, including a chairman and vice chairman.
