Mary Jean Lacaba, 37, has been turned over to authorities, and despite being weak from weeks in captivity, was otherwise unharmed, President Gloria Arroyo said.
"We are happy that Ms Lacaba is back with us and we hope the ASG [Abu Sayyaf group] will also release the other two hostages very soon," Arroyo said in a statement on 2 April.
Two other hostages, Eugenio Vagni of Italy and Swiss national Andreas Notter remain with the Al Qaeda-linked group.
The release came just days after a tense stand-off between the Abu Sayyaf and the military. The rebels had threatened to behead one of the hostages if the army did not pull out all its forces from the impoverished island of Jolo.
The Vatican, the Italian government, as well as the ICRC president have all issued appeals for the three to be released.
Marine Colonel Eugene Clemen said the Abu Sayyaf handed over Lacaba to Jolo Vice-Governor Nur Ana Sahidulla, who had earlier been granted access to the rebel camp to check on the hostages.
"She was very tired. They didn't have much to eat during captivity and the past few days were filled with anxiety after they were told they were going to be beheaded," Clemen said. "She is now resting and is having a medical check-up. She has also talked with her colleagues in the ICRC."
He said the gunmen had refused to allow the three hostages to contact their relatives during the stand-off. He would not disclose other details of the release, except that there had been a flurry of talks between intermediaries that led to the breakthrough.
The ICRC confirmed that Lacaba has been freed, and that "she appears to be in good health, although very tired and extremely worried for her two colleagues", who were still alive when she left the rebel camp.
"Although we're very happy that Ms Lacaba will soon be back with her family, we remain very concerned for our other colleagues," the ICRC said.
The Abu Sayyaf had not demanded any ransom for the three, although previous abductions attributed to them had led to millions of dollars changing hands.
From 1,500 in the early 1990s, the group's strength has now dropped to around 300 fighters due to military operations that have killed many senior leaders and followers. It is on the US government's list of foreign terrorist organisations, and is blamed for the deaths of two American captives seized from an island resort in 2001.
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