(CNN) -- Juan Martin Del Potro put on hold Roger Federer's hopes of qualifying for the ATP World Tour Finals by inflicting a second straight defeat on the Swiss maestro in the final of his hometown tournament in Basel.
Third seed Federer needed to win Sunday's showdown to seal his place in the end of season showpiece in London next month for the 12th consecutive time, but came up short in a three set encounter.
Top seed Del Potro, who will be a dangerous outsider in the British capital, won 7-6 2-6 6-4 in two hours 20 minutes, denying former World No.1 Federer his sixth title in the event and repeating his 2012 victory over him in the title match.
The Argentine won a tight first set which saw them exchange breaks before it went to a tiebreaker which Del Potro took 7-3.
Federer, who recently parted with coach Paul Annacone after a disappointing 2013, hit back to level the match as two breaks of service gave him the second set.
But he fell an early break down in the decider -- serving up two double faults in the same game -- and was unable to retrieve the situation as former U.S. Open champion Del Potro took his fourth title of the season.
"I'm sorry again to beat you here," he said apologetically at the trophy presentation. "He's the hero here and for me my biggest inspiration.
"You make history at every tournament you play. I'm proud to be playing at the same time as you."
The 32-year-old Federer must now beat South Africa's Kevin Anderson or Russian Mikhail Youzhny in his second round match at the Paris Masters next week to reach the finals.
It would enable him to tie Ivan Lendl's record for successive appearances in the finale of the men's season where he would be bidding for his seventh victory in the event, his last in 2011 with a final loss to Novak Djokovic in 2012.
Meanwhile, Zouzhny showed he is in fine form heading into Paris with a 6-3 7-5 victory over top seed and three time defending champion David Ferrer of Spain in the final of the ATP tournament in Valencia.