The Frenchman battled to a 7-5 7-6 (7-3) victory over Swiss maestro Federer in the final in Toronto.
It marked the 13th-seeded Tsonga's 11th ATP World Tour title and first since February 2013.
On his way to the title, Tsonga claimed the scalps of four of the world's top 10 - Novak Djokovic, Andy Murray, Grigor Dimitrov and Federer.
The 29-year-old will return to the top 10 for the first time since March after becoming the first Frenchman to win on Canadian soil.
Tsonga served 11 aces and gave second seed Federer no break-point opportunities during the 107-minute battle at the ATP 1000 hard-court event.
Both players were comfortable on serve in the first set, until Tsonga broke to 30 in the 12th game.
Tsonga wasted chances in the second, squandering break points in the sixth and eight games.
His next missed opportunity was a match point in the 10th, but he made no mistake from 3-3 in the tie-break as he ran away to claim the title.