Fatah, the oldest Palestinian party, is holding its first congress in seven years at a time when Abbas is seeking to quell dissent in the face of internal rivalries.
The 81-year-old has not publicly designated a successor, and the vote will be an indicator of the strengths and weaknesses of the various factions in Fatah.
Casting his ballot this afternoon, Abbas called the polling "democratic and transparent".
According to a recent poll, two-thirds of Palestinians are dissatisfied with Abbas and want him to resign.
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The 1,400 delegates voted at Abbas's Ramallah headquarters in the Israeli-occupied West Bank and also in the Gaza Strip where several dozen were stranded after Israel refused them passage through its territory to Ramallah.
They are to choose 18 members of the party's Central Committee, its highest body. Abbas will appoint another four.
The congress will also elect 80 members of the Fatah Revolutionary Council -- the party's parliament. Another 40 council members are directly appointed.
"After the counting of votes during the evening the results should be announced at the concluding session on Sunday," Congress spokesman Mahmoud Abu al-Hija said.
Analysts say the party's rival factions include supporters of Abbas's longtime rival Mohammed Dahlan, currently in exile in the United Arab Emirates.
Abbas was elected president in 2005 for what should have been a four-year term.
But there have been no elections since then, and with his hold on power drawing increasing internal dissent, observers say he is seeking to ready a successor.
Social networks and some local news media during the week published names of candidates in the vote who they say have prior approval from Abbas and were therefore guaranteed election even before polling began.
At the opening session on Tuesday, members re-elected Abbas party head by consensus.
Observers see the reduced number of delegates eligible to vote -- down from more than 2,000 in 2009 -- as part of a move to exclude Dahlan supporters.