They were released in a 'gesture of goodwill' after the repatriation to Israel last year of the remains of Zachary Baumel, an Israeli soldier missing since the 1982 war in Lebanon, the prisons' authority said.
As part of swap deal brokered by Russia, Israel on Friday announced the release of two prisoners including one convicted of spying.
According to a report by news agency AFP, the prisoners, Sidqi al-Maqt, Amal Abu Saleh, are residents of annexed Golan Heights in Israel.
They were released in a "gesture of goodwill" after the repatriation to Israel last year of the remains of Zachary Baumel, an Israeli soldier missing since the 1982 war in Lebanon, the prisons' authority said.
The spying convict name Maqt was jailed in 2015 for 11 years for spying, treason, contact with a foreign agent and transfer of information to the Syrian government while Amal Abu Saleh was jailed for the murder of a Syrian who crossed the Israeli border.
Saleh was due to remain behind bars until 2023.
Israeli authorities had promised the release of two Syrian prisoners after the repatriation of the remains.
According to Israeli media, the release of Maqt and Abu Saleh was delayed because the two men wanted to return to the town of Majdal Shams in the annexed Golan Heights, rather than travel to Syrian-held territory.
Maqt told Syrian state news agency SANA his release was "without conditions and that is a victory of the will of the Syrians over the will of the occupier".
SANA said Maqt had been released in August 2012 after 27 years in Israeli detention.
"He was re-arrested on February 25, 2015... after he documented cooperation between the Israeli occupying army and the terrorists of Al-Nusra Front," it said, referring to Syria's then Al-Qaeda affiliate.
After midnight, SANA said Abu Saleh has arrived at his birthplace of Majdal Shams.
Some 23,000 Druze still live in the part of the Golan Heights Israel seized from Syria in the Six-Day War of 1967 and later annexed in a move not recognised by most of the international community.