In the super tiebreaker, the Czechs won four straight points to lead 9-5 and clinched victory when Mladenovic netted a backhand volley.
It was the second Grand Slam title for Hradecka, who also won the 2011 women's doubles title, and the first for Cermak. They were beaten finalists at the Australian Open in January.
Nestor and Mladenovic led 4-0 in the first set as Cermak dropped serve in the opening game by netting three volleys and Hradecka double-faulted on break point. They took the first set when Cermak sent a forehand volley wide.
However, the Czechs bounced back by breaking Nestor in the opening game of the second. While serving for the second set, they rallied from 0-40 to even the match on a backhand volley from Hradecka.