Federer has battled with illness since his arrival in Brisbane last Sunday and requested a Thursday start to give him as much time as possible time to get over it.
The challenge, then, of backing up four days in a row to reach the final may have been too much against the towering, powerful Raonic, who won 20 net points to Federer's seven.
"You played great already last year, I thought the final was epic on many levels," Federer told Raonic in the post-match presentation.
"Now this year, you've got it, you deserve it.
"This year, it was a bit tougher (for me), I was a bit sick, but I'm still here in the final and I couldn't be happier."
Federer served at just 45 per cent in the first set, and that played into the hands of Raonic, who generated chances with hard, deep ground strokes that locked up the 34-year-old's movement.
A double-fault from Federer and then a backhand into the net gave the Canadian his first break at 5-4, before Raonic served successfully for the first set.
Raonic, a quarter-finalist at the Australian Open last year, spent time off court at 2-1 in the second set to seek treatment on his right leg, but he was able to hold serve upon his return despite four double-faults in the one game.
He then broke Federer for the second time and expertly closed out the match to seal just his second career win over the 17-time grand slam winner in 11 attempts.
- AAP