The top-seeded Argentine clinched the title when Federer could not return a tough forehand.
Federer looked to the home comforts and raucous support at Basel, where he is a five-time champion, to revive his difficult season. He's won just one title in the past 14 months.
Still, the sixth-ranked Swiss star edged closer to securing his place in the eight-man lineup at the ATP World Tour Finals in London starting next week.
Del Potro earned his fourth title this season, all on hard courts.
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