The brothers, who regained their No. 1 ranking by reaching the final, were the second set of American siblings to win this tournament after Venus and Serena Williams' win in the women's doubles.
Third-seeded Bhupathi and Knowles made a strong start, dominating at the net to break the second-seeded Bryans in the second and fifth games en route to winning the first set.
evening the match
The momentum changed in the second set when the Bryans held off three break points in the seventh game, and squandered one of their own in the eighth, before breaking to even the match.
The Bryans maintained the pressure, breaking in the second, fourth and sixth games to take the title in one hour and 38 minutes.
"It's fun to see the hard work pay off, but it's still a long year, we've got to keep it going for 52 weeks," Mike Bryan said.
The Bryans, who previously won here in 2006 and 2007, have been ranked No. 1 in the world four out of the past five years. They conceded their top ranking to Nenad Zimonjic and Daniel Nestor in the last match of the season-ending Shanghai Masters last November.
India's Bhupathi and Knowles of the Bahamas were playing for their first Grand Slam title together since beginning their partnership at the start of last year.