"Everyone is in a safe position. We left our (old) position but we brought all our arms," said Lieutenant Colonel Ramon Zagala.
An initial group of 35 Filipino troops were picked up from their position by UN armoured vehicles on Saturday after Syrian rebels attacked their comrades positioned about four kilometres (two-and-a-half miles) away, said Zagala.
The remaining 40 soldiers engaged the Syrian rebels in a "seven-hour firefight", but later walked to safety to a UN position just over two kilometres away, he added.
They later moved to Camp Ziouani behind UN lines, he said.
"There is no more standoff. All are safe," he told AFP.
The incidents came as fighting intensified between the Syrian army and opposition fighters near the frontier, where UN forces patrol a buffer zone between Israeli and Syrian lines.
UN Secretary-General Ban Ki-moon has condemned the capture of the Fijian troops and called for their immediate release.
The UN troops serve in the United Nations Disengagement Observer Force, which monitors a 72km long buffer strip between Israeli and Syrian troops as part of a 1974 disengagement agreement after the 1973 Middle East War.
The force has 1223 troops from six countries.
UN troops in the Golan Heights were held by Syrian rebel groups in two incidents last year, but were later released unharmed.
