The resumption of the fragile peace negotiations comes just hours after the release of the prisoners as a confidence-building gesture, and a day after Israeli authorities announced the approval of 942 new settler homes in annexed east Jerusalem, provoking Palestinian fury.
Jerusalem city authorities said that although it had only now granted final approval for the new homes in Gilo, an existing settlement in east Jerusalem, they had been in the works for years.
Senior Palestine Liberation Organisation official Yasser Abed Rabbo said the "unprecedented" announcements threatened to make the talks "fail even before they've started".
The last peace talks broke down in 2010 over the issue of settlement building.
More From This Section
In a bid to defuse the crisis, US Secretary of State John Kerry, whose dogged shuttle diplomacy brought about the first round of talks in Washington two weeks ago, phoned Abbas late yesterday, a senior source told AFP.
"We are waiting for the United States to take a clear stance on the escalating settlement building, which we consider the biggest obstacle that Israel is creating to stop serious talks from happening."
Abbas's office also confirmed he had received a phone call from Kerry "to discuss developments in the peace process, on the eve of the resumption of negotiations".
A group of 15 crossed into the Gaza Strip at about 1:40 am (2240 GMT) and were mobbed by relatives as they got out of a bus next to the border.
At about the same time, another 11 prisoners arrived in the West Bank city of Ramallah to a welcome from Palestinian president Mahmud Abbas and thousands of cheering, dancing supporters.
"This is the first group," Abbas told the crowd at an official welcoming ceremony at his Muqataa headquarters compound.
"We shall continue until we free all the prisoners from Israeli jails," he said.