Del Potro, who defeated the Basel native in three sets last October, repeated the feat Sunday, downing the Swiss icon 7-6 (7-3), 2-6, 6-4.
The Argentine's win in the 2012 indoors final had snapped a 2-13 skid against Federer, and he has since gone on to take three straight from the former world No. 1.
With the victory, Del Potro racked up his fourth title of the year -- following victories in Rotterdam, Washington and Tokyo -- as well as his 17th career crown.
He also was finalist at Indian Wells and Shanghai this year.
Federer, meanwhile, came up short in his fourth final of 2013. His lone win this season was at Halle, Germany.