The five released Palestinians, none of them involved in deadly attacks against Israelis, left the Hasharon prison and made their way to the West Bank, the spokesperson said.
The recent release, signaling the final stage of the UN-brokered swap deal with Hezbollah, was approved by the Israeli cabinet earlier this week.
Last month, Israel exchanged five Lebanese prisoners and the remains of 199 Lebanese and Palestinian militants for two bodies of Israeli soldiers captured by Hezbollah in 2006.
Sergeant Major Ehud Goldwasser and First Sergeant Eldad Regev were abducted by Hezbollah in July 2006 in a cross-border raid that sparked a month-long war in which more than 1,200 Lebanese civilians died.
Around 11,000 Palestinians are currently being held in Israeli prisons.
