General Gregorio Catapang told reporters that the pair had been taken to a military hospital after their release.
DXRZ radio, based in the city of Zamboanga, had earlier broadcast an interview with a spokesman for the hostage-takers, who claimed they had received a ransom payment.
TV station GMA News quoted an unnamed government official, who said that 60 million pesos (around €1m) had been paid to secure the hostages' release.
There was no official confirmation of the reports early on Friday afternoon. The Islamists had set a deadline of Friday for payment or one of the hostages would be killed.
The Foreign Ministry in Berlin had confirmed at a press conference earlier on Friday that one of its crisis negotiators was in the Philippines to deal with the case.
The 72-year-old German doctor and his 55-year-old partner, both from Hesse, were abducted in April while sailing around the islands, and have been forced to appear repeatedly in videos released online and on local radio.
Abu Sayyaf had been demanding a ransom of more than 250 million pesos (€4.4 million) for their release, as well as insisting that Germany cease all support for the battle against Isis in Iraq.
Earlier on Friday they announced a two-hour extension to their 7am deadline before beheading one of the couple if the payment of the ransom were promised over the phone.
Filipino armed forces were also reportedly preparing to rescue the pair, two anonymous soldiers told DPA. But officials wouldn't confirm the reports at the time.
Abu Sayyaf, classed as a terrorist organization by the United States, is a band of several hundred Islamic militants which started out as an offshoot of Al-Qaeda in the 1990s.
In a video released earlier this year, the group swore allegiance to Isis after the Iraq- and Syria-based terrorists claimed statehood.
It operates on remote and largely lawless southern Philippine islands that are mostly populated by the nation's Muslim minority, and has been blamed for some of the Philippines' most brutal terror attacks.
It is believed to be holding up to ten other hostages, including two European birdwatchers captured in February 2012.