Djokovic, who lost the world No. 1 ranking last week to Rafael Nadal  despite winning the China Open, topped del Potro 6-1, 3-6, 7-6 (7-3) in a 2 1/2-hour match. Djokovic won last year's Shanghai Masters also in a three-set final,
It was the sixth time in their last seven meetings that Djokovic beat del Potro but the matches have generally been close.
That was the case Sunday although Djokovic looked like he was going to win in a rout with a first set in which he had two breaks. Del Potro fought off three break points and recorded the only break of the second set to even the match but he had only one break opportunity -- saved by Djokovic -- in the third set.
Djokovic took the first two points of the tiebreaker and later led 4-2 before closing out his fifth championship for 2013 and 15th Masters-level tournament. He has 39 career ATP titles.
Del Potro, who was coming off a tournament win at last week's Japan Open, fell to 16-7 in ATP finals. He had won seven of his last eight title matches.
Djokovic collected $729,725 along with the Shanghai Masters title, pushing his career winnings past the $54 million mark. Only Roger Federer ($77.9 million) and Nadal ($60.9 million) have won more. Del Porto's runner-up check was for $357,000, giving him career winnings of about $13.9 million.