He served it out to take the opener in 41 minutes and the same pattern continued in the second set.
Federer managed just one break point as Raonic served four double faults in the fourth game after having a medical time out for a right leg injury.
The 17-time grand slam champion could not take advantage of the fleeting chance and was broken himself in the seventh game.
Raonic claimed the title when Federer hit a backhand long, an immediate boost to his fortunes after a disappointing 2015 campaign, which saw him suffer with foot and back injuries.
It was his eight career crown and revenge for a three-set defeat to Federer in last year's final in Brisbane.
In an added twist, Raonic's former coach Ivan Ljubicic has taken over the same duties with Federer, the Croat watching his defeat from a courtside box.
Raonic has paired up with former world number one Carlos Moya, who will be part of his team for the opening grand slam of the season in Melbourne. INTERNATIONAL NEWS - An ailing Roger Federer lost his Brisbane title to Milos Raonic Sunday as he slipped to a straights sets defeat to the big-serving Canadian.
Federer was hoping to match world number one Novak Djokovic, who began his 2016 campaign with a "perfect" performance to claim the Doha title 24 hours earlier, but came up well short.
The 34-year-old Swiss maestro had started the week with a flu bug, improving each round until he came up against fourth seed Raonic in the final on the Pat Rafter Arena, losing 6-4 6-4.
"I've still got a cough and the throat is a bit weird," he told reporters after his defeat.
"I've definitely got to make sure I get over it as quickly as possible."
