The group was part of a 72-member contingent situated in two different locations in the area.
Those remaining are currently still under fire, preventing them from being moved out, the UN said in a statement issued from its New York headquarters.
"The UN Disengagement Observer Force (UNDOF) reports that, early this morning, UN Position 69 was fired upon by armed elements," the UN said in a statement issued from its New York headquarters.
"The Mission's Force Reaction Group has been deployed to the position and all 32 Filipino personnel from this position have been extricated and are now safe."
The statement said another position was also attacked by "armed elements" with mortar and heavy machine gun fire and that the peacekeepers returned fire and prevented the attackers from entering.
UN chief Ban Ki-moon strongly condemned the attack on UN peacekeepers, by non-state actors he said included the Al-Nusra Front, Ban's spokesperson said.
Ban called for the immediate release of peacekeepers who had been detained, a call echoed later Saturday by a Security Council resolution.
However, "we are still working towards the safe release of the detained 44 Fijian peacekeepers," it added.
Speaking on condition of anonymity, UN soldiers said earlier that part of the encircled Filipino contingent had been brought out and that others were no longer in rebel hands but awaiting better security conditions so they could enter the Israeli-controlled part of the plateau.
In Manila, Philippines Defense Minister Voltaire Gazmin said UN peacekeepers had clashed with Syrian rebels.
Gazmin said in a statement to reporters that the Filipino troops had been "extricated" from one of their two positions but added that another group of Filipino soldiers "is now under attack."
The peacekeepers were besieged by rebels Thursday but defied demands that they give up their weapons.
Rebels, including some linked to Al-Qaeda's Syria affiliate, Al-Nusra Front, also took hostage 44 Fijian peacekeepers, the UN has said.