Fighters from the Nusra Front captured the Fijian troops late last month in the Syrian-controlled side of the Golan Heights, where a 1,200-strong UN force patrols the disputed buffer zone between Syria and Israel.
The area along the frontier has since been engulfed in heavy clashes between the militants and the Syrian military.
All 45 peacekeepers "are in good condition" and were being taken for a quick medical assessment, a UN statement said.
The hostage crisis raised questions about the future of the decades-old UN Golan mission, as participating nations threatened to pull their troops out because of Syria's escalating violence.
The Fijian troops were captured August 28, a day after militants seized control of the Syrian side of the Quneitra crossing from President Bashar Assad's troops.
UN Deputy Spokesman Farhan Haq said they were released at Syrian-side of the Quneitra crossing point near Israel. He told AP that they crossed into the Israeli-controlled Golan territory, were then taken to a UN post further north and would then go to Camp Faouar inside the Syrian-controlled Golan.
An unidentified peacekeeper expressed relief.
"We're all very happy to be safe and alive," he told the Israeli channel.
The same day the Fijians were taken captive, two groups of Filipino peacekeepers were trapped at separate UN encampments, surrounded by rebel fighters who demanded they surrender.
They refused, and both groups of Philippine troops eventually escaped, one busting out with the help of Irish colleagues, and the other by slipping away under the cover of darkness.
The U.N. Mission in the Golan Heights was established in 1974, a year after the Arab-Israeli war. Israel captured the Golan Heights from Syria in 1967, and Syria has demanded the return of the land in past peace talks.
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