An Israeli prison official said that another two were taken to the border with neighbouring Jordan and two more were released at Atarot in Israeli-annexed east Jerusalem.
"The International Red Cross Committee assisted in the process of conveying the prisoners," the Israeli military said in a statement.
It confirmed that 505 prisoners were transferred to the West Bank and 41 to the Gaza Strip with the remaining four taken to Jordan and east Jerusalem.
One of the Jerusalem residents freed was Salah Hamuri, 26, a French-Palestinian who was convicted of plotting to assassinate a Jewish religious leader and had been due to complete his seven-year sentence in March.
Speaking to AFP inside the car taking him home, Hamuri thanked those who had worked for his release.
French president Nicolas Sarkozy has long been pressuring Israel to free him.
"I want to thank all the people who were with me, with the struggle of the prisoners, with my struggle and the struggle of my family," Hamuri said.
"I promise that my release will be the beginning of the collective struggle for our common goal, the freedom of our people and the return of Palestinian refugees."
Also among those freed on Sunday were six women and 55 minors aged 14-17, according to UN children's rights agency UNICEF, which welcomed the youngsters' release.
Unlike in the first stage of the deal, which saw the release in October of 477 Palestinians including hundreds serving life for killing Israelis, Sunday's operation did not include anyone "with blood on their hands," officials on both sides said.
The flag-waving crowd in Ramallah filled the Muqataa presidential compound and spilled out into surrounding streets as Palestinian officials welcomed the returnees, but president Mahmud Abbas was not present as he was travelling to Turkey.
"Our happiness will not be complete until all the prisoners return home," Abbas chief of staff Tayeb Abdelrahim told the returning prisoners at the Muqaata.
Sunday's release leaves around 4,000 Palestinians still in Israeli jails, the vast majority serving time for security offences.
The list of prisoner names was published on Wednesday, and two appeals to delay the deal lodged by Israeli victims of Palestinian attacks were rejected by the Supreme Court, the second just hours before Sunday's release.
The names of the prisoners to be released were selected by Israel, and none of them belongs to the Islamist Hamas or Islamic Jihad movements.
Israeli officials said priority had been given to members of Abbas's secular Fatah movement.
Under the landmark swap deal agreed with Hamas in October, Israel agreed to free 1,027 Palestinian prisoners in exchange for Shalit, who had been held in Hamas captivity in Gaza for more than five years.
It was the first time in 26 years that a captured soldier has been returned to Israel alive.