Djokovic, the second-seed, scored a 6-4-, 4-6, 6-2 victory in Basel, Switzerland, his fifth win over the top-seeded Federer in 14 matches on the ATP Tour.
The Serb has won four events in 2009.
Federer had taken the title in Basel, where he once was a ball boy, three straight years and had not lost a set on his way to this year's final.
Djokovic won $432,980.
Copyright 2009 by United Press International.
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