A second group of Israeli hostages left Hamas captivity on Saturday after hours of delay had increased the anxiety of desperate families.
The Israeli military said 13 Israelis were released in Gaza and in exchange 39 more Palestinian prisoners were released by Israel in the West Bank. Hamas also released four Thai hostages.
The first releases took place smoothly on Friday, under a temporary four-day truce deal brokered by Qatar.
Urgent talks saved Saturday's handover.
The Israelis had been expected to be handed over to the Red Cross on Gaza's border with Egypt at 16:00 (14:00 GMT).
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The Hamas armed wing, the Qassam Brigades, said there were issues over the delivery of aid to northern Gaza and the selection criteria for Palestinian prisoners being exchanged for captives held by Hamas. Israel denied violating the terms of the deal.
Hamas spokesman Osama Hamdan said a total of 340 aid trucks had gone into Gaza since Friday, but only 65 had reached northern Gaza - which he said was less than half of what Israel had agreed on. Israel describes the north as a war zone and says the UN is responsible for delivering the aid.
Later a senior Palestinian official close to the talks confirmed Qatar's statement that the dispute had been resolved.
And Hamas voiced "appreciation towards Egypt and Qatar for ensuring the continuation of their temporary truce with Israel".
On Saturday evening some 50,000 people rallied in central Tel Aviv with the slogan "Bring them back home" on posters and t-shirts, hoping that the fragile truce would hold.
The Israeli government said Saturday's handover freed two teenage members of the Or family; two members of the Weiss family (53 and 18); two members of the Avigdori family (52 and 12) and four members of the Haran and Shoham families, including a three-year-old and eight-year-old.
The father of Irish-Israeli Emily Hand, who turned nine while in captivity, told the BBC that while he was happy to have his daughter returned, he was determined to keep doing everything he could to help bring those still kept hostage home.
They include Raya Rotem, whose daughter, Hila Rotem Shoshani, was released on Saturday without her. Itay Regev, the brother of newly freed Maya, 21, also remains a hostage.
"My heart is split because my son, Itay, is still in Hamas' captivity in Gaza," said their mother, Mirit Regev.
Most of the 39 Palestinians released by Israel on Friday - 24 women and 15 teenage boys - were in pre-trial detention. One of them, Sarah al-Suwaisa, said the Israelis had fired teargas and cut off the prisoners' electricity before the release. She called it "humiliating, psychological torture" and said "only Hamas helped us".
Meanwhile, Thailand's Prime Minister Srettha Thavisin said that the four Thai nationals released on Saturday were doing well.
"Everybody is safe, on the whole in good mental health and are able to speak normally," he wrote on social media.
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