In a televised address on Sunday evening, US President Donald Trump had announced that "the world's number one terrorist leader" died during a "dangerous and daring night-time raid into northwestern Syria" by US Special Operations forces on Saturday.
His body was mutilated in the blast and the US troops had to dig through debris to reach his corpse. Soldiers conducted a DNA test using a small field kit to confirm his identity.
Baghdadi's remains have been disposed off in the sea.
The terrorist's underwear and a blood sample were used to match his DNA, The Daily Mail reported on Monday citing Syrian Democratic Forces (SFD) General Mazloum Abdi as telling NBC News.
Abdi said they had a source undercover in Baghdadi's inner circle who had direct access to the IS leader.
The source gave US intelligence a pair of Baghdadi's used underwear and a blood sample at some point this year.
US soldiers used the DNA from those samples to positively identify him from the remains found in the compound after the blast. That same source was at Baghdadi's compound when it was raided and he left with US forces, Abdi added.
When Al Qaeda leader Osama bin Laden was killed by US Navy Seals in Pakistan in May 2011, US forces had to send his remains off to an American lab in Afghanistan to confirm his identity via DNA.
Baghdadi's DNA was confirmed to be a match within about 15 minutes, according to President Trump.
The White House said that Baghdadi was identified via both DNA tests and visual evidence.
His head was reportedly still intact, which meant a bio metric facial-recognition scanner was used to identify him, The Daily Main said in its report.
Baghdadi, who was in his late 40s and carried a bounty of at least $25 million, was one of the most wanted terrorists in the world.
He presided over the brutal 'Caliphate' that he had set up in Syria and Iraq enforcing a fundamentalist code and killing thousands.
( With inputs from IANS )