The 33-year-old Swiss joins Jimmy Connors and Ivan Lendl as the only players in the modern professional era to achieve that feat and was claiming his 83rd career title.
Federer led by a set and 2-0 until Raonic broke back and reeled off seven straight points in the tiebreaker to level at a set all.
The third set might have gone either way, with top seed Federer staving off five break points, but a single break of the Raonic service proved decisive and he completed victory in two hours 13 minutes.
It completed a fine week for the world number two as he prepares for a tilt at the upcoming Australian Open title in Melbourne.
By contrast, his arch-rivals Novak Djokovic and Rafael Nadal slipped to early round defeats at the ATP event in Doha to disrupt their preparations for the opening grand slam of the season.
Federer, who was surprisingly beaten in the final of the corresponding event by Lleyton Hewitt last year, was winning the Brisbane title for the first time.
He extended his career record over the emerging Raonic to 8-1 with his latest triumph, but still has ground to make up on former greats Connors (1,253 wins) and Lendl (1,071).
At the presentation he was awarded the trophy by Roy Emerson and a special award for 1,000 wins by fellow Australian legend Rod Laver.
"To get to 1,000 wins in front of you two greats means a lot to me," Federer said.
"I'll never forget this moment."
Wawrinka doubles up
In other ATP final action Sunday, top seed Stanislas Wawrinka successfully defended his title at the Chennai Open in India.
Federer's compatriot Wawrinka, who is preparing for his defense of the Australian Open title, beat Slovenian qualifier Aljaz Bedene 6-3 6-4 in 69 minutes in the final.
The 29-year-old Wawrinka also won the title at the hard court event in 2011.
It was his eighth career tournament victory and earns him 250 ranking points.