The 36-year-old local favourite, beaten by Del Potro in consecutive Basel finals in 2012 and 2013, was ragged at times and looked in danger of an unwanted hat-trick, but showed all his fighting qualities to turn the match around.
Fourth seed Del Potro, making a late run to try and qualify for next month's ATP World Tour Finals in London, broke serve in the first game of the decider but wilted as Federer stormed back to the delight of a raucous crowd inside the St Jakobshalle.
World number two Federer charged into a 5-2 lead and while Del Potro delayed the end by holding serve, Federer would not be denied and racked up his 95th career title as Del Potro fired a backhand long under pressure.
In edging past Ivan Lendl's 94 Federer is now alone in second place on the all-time titles list which American great Jimmy Connors leads with 109.
However, his chances of snatching the world number one ranking from Rafael Nadal before the end of the season are all but over as the Swiss pulled out of next week's Paris Masters citing a back injury.
Federer, who trails Nadal by 1,460 points in the rankings, has taken regular breaks during the season to rest his body and no doubt opted to skip the Paris tournament to prepare for next month's ATP Finals in London.
Del Potro would have moved into the eighth and final qualifying spot for London had he claimed a third Basel title, but now must reach the semi-finals at least in the French capital to make it to the season-ending tournament.
"All the best for Paris and then I'll hopefully maybe see you in London, too," Federer said after an intense battle with the 29-year-old Argentine who fell just short of claiming a second successive title after winning in Stockholm.
Federer broke serve in the opening game but Del Potro hit back immediately when Federer netted a backhand.
Del Potro struggled to hold serve and cracked at 4-4 under a flurry of Federer winners. Federer could not serve out the set though and was broken as Del Potro took it to a tiebreak.
Federer went 3-0 up but lost six successive points. He saved two set points but Del Potro took the opener on his third chance -- leaving Federer flustered.
The 19-times grand slam champion smashed his racket into the net at one point during the opening set, but it was Del Potro's turn to lose his cool when he dropped serve at 4-5 in the second as the crowd roared Federer on.
Del Potro took the opening game of the decider but looked fatigued as Federer found another gear to surge back.
(Writing by Martyn Herman; Editing by Christian Radnedge and Pritha Sarkar)
source: news.abs-cbn.com
