Mokhtar Lamani, the Damascus representative of the new UN-Arab League peace envoy to Syria, said the peacekeepers crossed into Jordan on Saturday afternoon, Reuters reported.
Yarmouk Martyrs brigade, a rebel group, claimed responsibility for the kidnapping.
Syrian rebels initially said they would only release the hostages once Syrian troops withdrew from the area. However, rebels eventually dropped their demand and began negotiations with U.N. officials to free the peacekeepers.
On Friday, a U.N. team tried to free the hostages, but was unable due to heavy regime shelling of the area.
On Wednesday, armed elements of the Syrian opposition detained a group of peacekeepers who are part of the UN Disengagement Observer Force (UNDOF), which monitors the 1974 disengagement accord between Syria and Israel after their 1973 war.
The UN estimates that the Syrian conflict has claimed more than 70,000 lives and forced millions from their homes.
Israel seized the Golan Heights during the 1967 Six-Day War. UN peacekeepers have been monitoring the armistice line that followed the 1973 Arab-Israeli war, in which Syria tried to recapture the territory.
Earlier, Israel warned that it will not “stand idle” as Syria’s civil war spills over into the Golan region.