Military chief General Gregorio Catapang called it "the greatest escape," and praised the soldiers.
"Although they were surrounded and outnumbered they held their ground," he told reporters.
The troops are part of a UN peacekeeping force which has been stationed in the Golan Heights since 1974 to monitor a ceasefire between Israel and Syria.
"Everyone is in a safe position. We left our (old) position but we brought all our arms," said Lieutenant Colonel Ramon Zagala.
The remaining 40 soldiers engaged in a "seven-hour firefight" with rebels who tried to ram the gates with pick-up trucks carrying anti-aircraft guns. The troops later walked to safety to a UN position just over two kilometres away.
In a statement, the UN said the 40 Filipino peacekeepers withdrew shortly after midnight "during a ceasefire agreed with the armed elements".
They later moved to Camp Ziouani behind UN lines.
The troops, burdened by their equipment and the cold weather, walked for about an hour and 40 minutes in the dark to reach safety, he said in Manila.
Military chief Catapang said the Syrian and Israeli governments had supported the Filipinos in upholding "the integrity of the area of separation".
Catapang also credited the US and Qatar governments for helping safeguard the blue helmets but did not elaborate.
"The Armed Forces of the Philippines and the United Nations will not compromise the safety and security of our troops while in the pursuit of their duties.
The head of Philippine peacekeeping operations, Colonel Roberto Ancan, said the Syrians had provided "indirect fire support" that took the pressure off the besieged Filipinos.
The peacekeepers were besieged by rebels Thursday but defied demands that they give up their weapons.
