Top seed del Potro beat third seed and five-time former champion Roger Federer 7-6(3), 2-6, 6-4 in a repeat of last year’s final. The high-quality championship match lasted two hours and 21 minutes.
The 25-year-old Del Potro has also won ATP World Tour 500 tournament titles in 2013 at the ABN AMRO World Tennis Tournament in Rotterdam (d. Benneteau), the Citi Open in Washington (d. Isner) and the Rakuten Japan Open Tennis Championships in Tokyo (d. Raonic).
Del Potro has already qualified for the Barclays ATP World Tour Finals, to be held at The O2 in London from 4-11 November.
But Federer must now beat Kevin Anderson or Mikhail Youzhny in his second round match at the BNP Paribas Masters in Paris on Wednesday to qualify for a record-equalling 12th consecutive year. It would tie Ivan Lendl for most successive appearances at the season finale.
Del Potro has now won 17 trophies. He received €348,000 and 500 Emirates ATP Ranking points after he improved to a 23-1 match record at ATP World Tour 500 tournaments this season. Federer, now 5-5 in Basel finals, picked up €156,800 and 300 points.
It was their 18th meeting and Federer was attempting to win six or more titles at his fourth different tournament. He has won six or more crowns at Wimbledon (7), the Barclays ATP World Tour Finals (6) and the Gerry Weber Open in Halle (6).
Mikhail Youzhny won his second ATP World Tour crown of the season with a 6-3, 7-5 victory over defending champion David Ferrer in the final of the Valencia Open 500.
It was Youzhny's 10th career title and first victory over a Top 5 opponent since 2010, when he upset Novak Djokovic in the Rotterdam semi-finals. The World No. 21 also prevailed on the clay of Gstaad in July.
The Russian has won multiple titles in one year for the first time since 2010, when he hoisted the trophies in Munich and Kuala Lumpur. He also added to the impressive title count of players over 30, in 2013, becoming the fourth such player to win multiple titles this year, joining Ferrer,Tommy Haas and Nicolas Mahut. In total, 16 players over the age of 30 have won on the ATP World Tour this year, three more than last year's tally.