A Palestinian security source confirmed on Friday that eight of the 12 had arrived in the Gaza Strip.
The Israeli Supreme Court had given the go-ahead for the expulsions on Thursday, and a military spokesman said the measures were carried out between Thursday evening and early on Friday.
He said the Palestinians, who had been imprisoned without trial, had been taken in groups of four via a military base near to their place of detention and the Erez crossing point between the Gaza Strip and Israel.
The spokesman said eight were members of the Palestinian resistance group Hamas, three belonged to the smaller Islamic Jihad and the 12th was a member of an armed group linked to Palestinian leader Yasir Arafat's Fatah movement.
Ghanim Sawalmeh, 30, from the Balata refugee camp next to the West Bank city of Nablus, told reporters he was glad to be "free in part of my homeland," but he objected to being cut off from his family, including a baby girl born one month before he was arrested in June 2002.
Sawalmeh, a teacher, was never charged.
"We are victims of the occupation policy and the occupation aggression against our people," he said after arriving at Gaza police headquarters.
The army had decided to banish a total of 18 detainees from the West Bank to the Gaza Strip for between one and two years. Five were transferred last month and put under house arrest, while the 18th is still in administrative detention.
Palestinian legal experts say the measure violates article 49 of the Geneva Convention banning forced displacements.
West Bank Palestinian Ghanim
Sawalmeh arrives in Gaza City
The Palestinian Centre for Human Rights on Thursday condemned the practice.
"PCHR calls upon the Israeli military to immediately rescind these 'assigned residence' orders and halt all other grave breaches of international humanitarian law," the group said in a statement.