The top seed beat the five-time former champion 7-6 2-6 6-4 in a repeat of last year's final in a match which lasted two hours and 21 minutes.
Federer was hoping home advantage would help him secure a victory which would earn him a place in the ATP World Tour Finals in London early next month.
"I was lifting my level and in the end I wasn't playing too badly," Federer said at the trophy ceremony.
The Swiss must now beat Kevin Anderson or Mikhail Youzhny in his second-round match at the Paris Masters on Wednesday to equal Ivan Lendl's record of 12 consecutive appearances at the season finale.
Earlier Britain's Dominic Inglot won his second ATP World Tour doubles title with Filipino partner Treat Huey.
Inglot and Huey won their first title in Washington last year and had come out on the losing side of three further finals this season.
But they recovered from losing the second set to Austrians Julian Knowle and Oliver Marach to win 6-3 3-6 10-4 on a match tie-break.
The victory also kept alive their slim hopes of qualifying for ATP World Tour Finals in London heading into next week's Paris Masters.