The German man and woman were seized in April when their yacht had mechanical problems while sailing from western Palawan in the Philippines to the eastern Malaysian state of Sabah.
Military and government officials could not immediately confirm the report.
The rebels had demanded a 250 million pesos ($5.6 million) ransom and for Germany to stop supporting US-led air strikes in Syria. They had originally threatened to kill one of the captives on Friday afternoon.
"A few minutes ago, we released the two Germans," said Abu Rami, spokesman for the small but violent Abu Sayyaf group, in a radio interview. The group said that the ransom was paid in full.