Berdych, fresh off his quarter-final upset of No 2 seed Andy Murray, started well and held his first five service games, although neither player was able to secure that all-important break of serve.
However, the resurgent Nadal finally made the breakthrough in the 11th game, taking the first break point of the set - avoiding the tie-breaker in the process.
The Spaniard raced into a 40-0 lead on his serve to secure three set points, although Berdych showed some fighting spirit by saving two. However, at the third time of asking Nadal clinched the first set 7-5.
The players held serve to start the second and Nadal tried to turn the screw in the third game. The French Open champion piled on the pressure by moving 40-15 in front, but some big serving from the Czech ace turned the game around.
Berdych had a break point in the sixth game of the second set, but a long forehand gave Nadal a stay of execution. He did however take his second and move 4-2 in front following a loose forehand by the Spaniard.
But Nadal responded in champion fashion by breaking back at the first time of asking to square the second set - a series of powerful forehands proving too much for his opponent.
Berdych was unable to convert four break points in the ensuing game to allow Nadal to square up the second set at four-games apiece.
The quality of the tennis increased as the match progressed. Berdych eventually moved 6-5 in front, but only after a marathon game that lasted seven minutes and 19 seconds.
Nadal held serve to force a tie-breaker and it was the Spaniard who triumphed when it mattered, taking the set 7-6 and ultimately the match.