The clashes came about after militants had surrounded the peacekeepers encampment, said officials and activists, as the organization risked becoming more involved in the conflict.
Other peacekeepers from the UN were able to flee a different nearby encampment that had also been surrounded by Nusra Front rebels an affiliate of al-Qaeda.
The Defense Secretary of the Philippines confirmed that some of the peacekeepers that were extricated were from his country.
The clashes took place after rebel groups from Syrian overran the crossing at Quneitra, located on the border between the Israeli and Syrian controlled areas of the Golan Heights during midweek, detaining 44 peacekeepers from Fiji.
The Nusra Front surrounded the Breiga and Rwihana encampments where there were other peacekeepers from the UN holed up.
A battle began Saturday where 40 peacekeepers from the Philippines had been surrounded by fighters from Nusra who had ordered them to surrender.
Witnesses said they did not know of any fatalities amongst the peacekeepers in the encampment. A military spokesperson from the Philippines also said no casualties had been suffered.
However, peacekeepers in the other encampment of Breiga fled, but no one is certain to where or how many were able to escape.
The rebels from Nusra Front have been seizing hostages in exchange for their members who have been detained in Lebanon and Syria.
The UN said that it had been given assurance from source that were said to be credible that the peacekeepers from Fiji were safe.
The statement from the UN added that the intention for detaining the peacekeepers had been to remove them from the active battlefield to an area that was safe for their protection.
The Foreign Minister of Australia condemned the peacekeepers detention and called for them to be released immediately.
The Secretary General of the UN Ban Ki-moon also condemned their detention and called for their release immediately.