The top-seeded Bryans faced two break points in the ninth game of the first set Saturday before winning the opener when Zimonjic hit a backhand long.
Zimonjic and Nestor were down 5-2 in the tiebreaker before winning five straight points to take the second set.
In the decider, the Bryans got a service break in the fourth game, went up 4-1 and celebrated their win with a brotherly hug at the net.
The U.S. pair have won the title four of the past five years. They have eight Grand Slam men's doubles titles.
As if it wasn't confusing enough to tell the identical Bryan brothers apart, all four players on court were wearing red shirts and white shorts.
Nestor and Zimonjic took over the No. 1 doubles ranking from the Bryans in 2008, the only year of the past five the Americans have not ended as the top-ranked pair. Nestor and Zimonjic have an 8-4 record against the Bryans, including last year's Wimbledon final.
The Bryans regained the No. 1 ranking at the end of last year.