Four of those men, however, were no longer going to be freed, Al Jazeera's Nour Odeh, reporting from the Beitunia, said.
"We've been reminded repeatedly today that almost 11,000 Palestinians remain behind Israeli bars," our correspondent said
"So a bittersweet moment, not just for Palestinians across the board, but even for those waiting for their loved ones [at Beitunia], knowing that their friends are still behind bars."
Israel's supreme court approved the release on Monday, hours after the plan was thrown into doubt by judges who had ordered the release delayed until the state replied to a petition against it.
Israel decided to free the prisoners as a gesture of support for Abbas, coinciding with the Muslim festival of Eid al-Adha.
All the prisoners to be freed are members of Fatah's armed wings, or other smaller groups, and none of them are from Hamas.
Israel has said the periodic release of small numbers of Fatah prisoners is aimed at boosting support for Abbas in his power struggle with Hamas.
The release was supposed to have taken place last week, but was postponed.
Israel said the delay was due to a request from the Palestinians, although Palestinian officials denied this.
In another development, senior international officials have written a letter to the Israeli prime minister, arguing that Israeli restrictions on cash shipments to Gaza banks, meant to weaken the territory's Hamas rulers, are largely counterproductive and ultimately harm Palestinian moderates.
Israel imposed restrictions on Gaza after Hamas seized the territory in June 2007, ousting Fatah supporters.
Israel declared Gaza a "hostile entity" and largely sealed its borders, allowing in only humanitarian supplies and a trickle of commercial goods, while banning exports from Gaza.
The letter to Ehud Olmert was signed by Robert Zoellick, the World Bank president; Dominique Strauss-Kahn, the International Monetary Fund's managing director; and Tony Blair, the international Middle East Quartet's envoy.
The three also expressed concern about a decision by two Israeli banks to sever correspondent relationships with their Palestinian counterparts.
The two developments "may have a considerable impact on the Palestinian economy and its institutions, and ultimately on Israel's longer-term relationship with the Palestinians", the letter said.