Brothers Michael Ray Stubbs, 55, and Jamil Daud Mujahid, 56, were turned over Saturday to American marshals who escorted them back to the United States.
Both were blacklisted as "undesirable aliens and threats to national security," the bureau said.
The two had been in detention since December after being arrested south of Manila.
Authorities said the suspects were earlier seen meeting with leaders of the Abu Sayyaf and the separatist Moro Islamic Liberation Front (MILF).
The Abu Sayyaf is a small group of self-styled militants blamed for a series of bombings and kidnappings in Mindanao in recent years.
The MILF has been waging a rebellion for the establishment of an independent Islamic state in the southern third of the mainly Roman Catholic Philippines.
The US and Philippine governments have branded the Abu Sayyaf a terrorist organization, whose leaders once had loose links with Saudi dissident Osama bin Laden’s al-Qaeda network. The military, meanwhile, has accused the MILF of training foreign Jemaah Islamiyah (JI) militants.
The JI is said to be the Southeast Asian arm of al-Qaeda and has been blamed for the October 2002 bombings in Bali, Indonesia that killed over 200.
The immigration bureau said Mujahid, a Muslim convert whose former name was James Stubbs, once worked as a teacher in Missouri.
In May 2003, Mujahid began meeting with leaders of local groups, it added.
His brother is an air-conditioning technician who worked for the Lawrence Livermore National Library, which is helping the US Department of Homeland Security in promoting research on nuclear and radiological weapons.
Ray Stubbs is also a computer expert who Philippine authorities say maintained bank accounts with substantial deposits from dubious sources. — AFP