The prolific competitors were evenly matched at the start of the first set with games going by the way of serve, but Federer came the closest to grabbing the first break.
The Swiss pro went 30 to love up in the fourth game, but Nadal managed to battle back to hold serve and keep proceedings level in the opening set.
Then it was the Spaniard's turn to take advantage, but he squandered two break points to keep Federer in the game as both players struggled to find the breakthrough.
The set was eventually decided by a tie-break, and it was Nadal who managed to take his chances and grab a one-set lead with a 7-4 in the decider.
The start of the second set was interrupted for a short period of time while Nadal sought treatment on the blisters on his hands, but it failed to trouble the Spaniard, who had the first opportunity of a break.
Federer was able to hold out once again, but not for long as Nadal managed to get the first break point on the board, putting himself in control of the second set.
Despite some swift shots across the court from Federer, he struggled to launch a comeback in the second, resulting in Nadal doubling his lead.
The Swiss pro had it all to do in the third, but Nadal kept his opponent on the back foot by taking an early break point.
However, Federer put up a fight by breaking back instantly, taking his first break point after two hours and two minutes of play, but unfortunately for the sixth seed, it didn't last long.
The world number one broke Federer to give himself the edge, and then broke serve for the third time in the set to win the match.