Rogers Federer retains Basel title
The Swiss star had lost his five previous matches against Nadal and appeared in danger of another defeat when he dropped the second set, but took a decisive break in the third to seal a 6-3 5-7 6-3 win on home soil.
Nadal has shown new-found confidence throughout the week and quickly scrutinised the Federer serve, bringing up an early break point which was repelled by his long-time rival.
Federer was far more clinical with his next break point opportunity as a pinpoint forehand allowed him to move 4-2 up in the opener.
With Nadal pushing for a break back, Federer fired another forehand winner to preserve his serve and then snatched a second break to seal the set.
But the Spaniard has shown his usual battling spirit in recent months and took his third break point chance to move 6-5 up in the second set.
A fizzing forehand into the corner kept Federer at bay in the next game and Nadal would level the match with a fierce slam.
Both men refused to give ground in the early stages of the decider, with Federer unloading sweetly-struck ground strokes while briefly troubled on his serve.
Nadal could not keep his old foe at bay in the eighth game and was broken after sweeping a forehand into the net.
But Federer was still forced to work for his seventh title win as Nadal fended off one match point before firing long to confirm his defeat.