The 25-year-old Canadian lost to 17-time Grand Slam champion Federer in three sets in last year's final.
But Raonic produced an impressive display at the Pat Rafter Arena on Sunday to clinch his eighth tour title.
Federer, who has been suffering with flu, said: "I'd like to congratulate Milos on a great start. This year you deserve it, well played and good luck at the Aussie Open."
The Swiss world number three added: "I was a bit sick but we made it to the final."
Raonic, who is ranked 14th in the world, had only beaten Federer once in their previous 10 encounters.
He said after his victory: "Hopefully we have a better year this year than the last. I hope in 2016 we learn to love each other a little bit more and the world becomes a safer place."
The Brisbane tournament helps players prepare for the Australian Open - the first Grand Slam of the year - which starts on 18 January.
Milos Raonic beat Roger Federer 6-4 6-4 to win the Brisbane International.