Voting was delayed for several days amid rows over the process
Younger leaders have gained powerful posts in Palestinian leader Mahmoud Abbas's Fatah faction, early results from its first poll in 20 years show.
Mr Abbas remains the head, but several veterans apparently lost seats on the powerful central committee.
Popular jailed leader Marwan Barghouti, and influential Mohammad Dahlan, who is disliked by supporters of rival faction Hamas, were both set to gain seats.
Young members wanted to depose an "old guard" seen as divided and corrupt.
The party, which lost elections to Hamas in 2006, has been trying to restore its image. It is widely seen as ineffective and dominated by cronyism.
Fatah has long been split between the ideologically-driven contemporaries of the movement's founder Yasser Arafat, who have spent years exiled overseas, and younger, more pragmatic, locally-born leaders who have negotiated with Israel.
Preliminary results from the vote during the congress in the West Bank town of Bethlehem showed new officials had gained 14 out of 18 seats on the powerful central committee.
Heather Sharp, BBC News, Jerusalem
Finally, the vote was held, after a long week, dogged by rows and factions' fears that their rivals had stacked the conference with sympathisers.
Palestinians may be heartened that Fatah got this far, and the sway of ageing exiles who do not share their daily struggles has been reduced.
But the so-called "new blood" are all established players in Palestinian politics, and still have a lot to prove if they are to convince voters they have left behind the days of corruption and infighting under Arafat.
While they broadly agree on a two-state solution, there are differences over Hamas. Mr Barghouti's supporters want to push harder for unity - and he remains in jail in any case - while Mr Dahlan is at the forefront of the feud.
Elections slated for 2010 will not happen without some kind of deal with Hamas. So for most Palestinians, a unified leadership with a popular mandate to fight their cause on the international stage remains as far off as ever.
Only four of the 10 members of the so-called "old guard" managed to hold onto their seats on the central committee, the results showed.
The Fatah veteran Ahmed Qurei, who was the first Palestinian prime minister, was on course to lose his seat.
One member of the founding generation, Muhammad Ghneim (also known as Abu Maher Ghneim), who is considered close to Mr Abbas and recently returned from Tunisia, appeared to have won a seat.
Saeb Erekat, a key negotiator with Israel, and Jibril Rajoub, who like Mr Dahlan has led one of the party's security forces, also gained posts on the committee, the partial results showed.
Mr Rajoub said the result was "a coup against a leadership that had monopolized the movement for a long time without even presenting a report about its work".
Election results for Fatah's other ruling body, the Revolutionary Council, are expected later on Tuesday.
Mr Barghouti and Mr Dahlan are the best known of the new members.
Mr Barghouti was a popular grassroots leader during the intifada or uprising that began in 2000 and has been seen as a potential unifying successor to Arafat.
But he is currently serving five life terms in Israel for organising attacks in Israel. He denies the charges and has said he opposes attacks on civilians in Israel.
Mr Dahlan was the head of a Fatah security force in Gaza, which was forced to leave after fighting with Hamas in June 2007.
He was strongly disliked by Hamas and other Islamist groups before that, after he led crackdowns against them.
The congress on Saturday elected Mr Abbas unopposed as the party leader, a post which he has held since the death of Arafat, in 2004.
The conference, which began last Tuesday, dragged on an extra five days amid rows over voting procedures and the outgoing central committee's failure to give a written report of its activities and spending over the past 20 years.
Hamas blocked about 400 delegates from leaving Gaza, and there were protracted disagreements about how their votes should be registered.
International observers have been watching to see if Fatah, which committed itself to peace negotiations in the early 1990s, would rule out armed struggle.
The conference discussed proposed revisions to Fatah's charter, although the document has yet to be finalised.
Delegates said the new wording would not abandon the old document's call to "liquidate the Zionist entity", but would include a commitment to "two states for two people".
It would call for a Palestinian state be established on the basis of 1967 borders - meaning all of the West Bank and Gaza - and maintain the "right to resistance" by all means, delegates said.
Fatah was founded in the 1950s to lead armed struggle against Israel, but effectively rejected violence and endorsed a two-state solution to the conflict by backing the Oslo peace process in the early 1990s.
During the conference, delegates' generally held to Fatah's existing demands for the release of all Israeli-held Palestinian prisoners, a capital in Jerusalem, the removal of all Israeli settlements in the West Bank, and the right of return for all Palestinians who fled or were forced out during Israeli-Arab wars.
Israeli Foreign Minister Avigdor Lieberman said Fatah's "radical and uncompromising positions" created an "unbridgeable gap between us and them".