Andy Murray and Rafael Nadal in Japan Open final
Murray overcame losing the first set to win his second straight ATP tour victory.
Murray, who also won last week in Bangkok, broke his Spanish opponent in the fourth game of the second set and then proceeded to win 11 of the next 12 games to clinch the title at Ariake Colosseum.
Nadal, the defending champion, had beaten Murray five straight times entering the match, and had not lost a service game in the tournament.
The title was Murray's fourth of the season after triumphs at Queen's Club, Cincinnati and in Thailand.
The match turned for good in the fifth game of the second set. After being broken in the previous game, Nadal squandered four break points and fell behind 4-1.
Murray pressed his advantage after the break, pressuring Nadal the rest of the way.
In the final set, Murray broke Nadal three times, behind a combination of forehand winners and unforced errors by the Spaniard.
The victory gave fourth-ranked Murray his 20th career ATP tour title.
Nadal is now 3-7 in finals this season, with the first six of the losses coming to Novak Djokovic.