Federer was forced to absorb some superb shotmaking and blistering serves from the 24-year-old before winning 6-4, 6-7 (2/7), 6-4 in two hours and 13 minutes at the Pat Rafter Arena.
Federer's glittering career now includes 83 singles titles, including 17 Grand Slams, since his first victory over Frenchman Guillaume Raoux in Toulouse in 1998.
The 33-year-old is third on the all-time list for matches won, behind Jimmy Connors (1,253) and Ivan Lendl (1,071).
"To get to 1,000 wins in front of you two greats means a lot to me," Federer said, describing it as a "special day".
"I'll never forget this moment," he added as he was presented with his Brisbane International trophy by Roy Emerson, as well as a special award for his 1,000th win by Rod Laver. "It feels very different to any other match I've ever won, because I never thought about anything reaching 500 or 800.
"All those numbers didn't mean anything to me, but for some reason 1,000 means a lot because it's such a huge number. Just alone to count to 1,000 is going to take a while."
Federer's big win was not a foregone conclusion. Raonic played so well that for long periods during the second and third sets it looked like the milestone would have to wait until next week's Australian Open.
But serving at 4-5 in the third set the Canadian faltered, giving Federer championship point with a double fault, before a forehand into the net ended the contest.
Federer said the nature of the match made the 1,000th win even sweeter.