The brothers, who regained their No. 1 ranking by reaching the final, were the second set of American siblings to claim Grand Slam titles after Venus and Serena Williams won the women's doubles.
"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 lost their top ranking to Nenad Zimonjic and Daniel Nestor in the last match of the season-ending Shanghai Masters last November.
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.
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 brothers maintained the pressure, breaking in the second, fourth and sixth games to take the title.
"Mahesh and I played very well, we just weren't able to close there at the end,'' Knowles said. "But they're worthy champions and we enjoy competing against those guys.''
India's Bhupathi and Knowles of the Bahamas were playing for their first Grand Slam title since beginning their partnership at the start of last year.
The final was a rematch of last year's quarterfinal, when Bhupathi and Knowles dealt the Bryans their first loss at Melbourne Park in three years. The Bryans won all four of their subsequent meetings, including earlier this month at the Sydney International semifinals.
Bhupathi has previously won four Grand Slams doubles titles with longtime partner Leander Paes and Max Mirnyi, while Knowles came to Melbourne with three titles, all with Daniel Nestor.
Bhupathi has another chance at a title in Melbourne when he joins fellow Indian Sania Mirza against Czech pair Iveta Benesova and Lukas Dlouhy in the mixed doubles final Sunday.
The 30-year-old Bryans have contested the Australian Open final five out of the past six years, and are only the fourth doubles team in the Open Era to win 50 ATP titles or more. The Australian title was their 51st.
Bryan brothers of US win Aussie doubles title
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