Del Potro picked up a win over first-seeded Rafael Nadal earlier in the day. Nadal felt pain in his right knee in the opening stages of the match and eventually stopped play after losing the first two sets.
"That was not a tennis match at the end. Just one player playing, the other staying on one side of the court," Nadal told reporters after the match. "I hate to retire, but staying one more set out there, playing like this, would be too much for me."
Del Potro held a 7-6 (3), 6-2 lead after two sets when Nadal could not continue. Nadal has a history of knee tendinitis and has cited the issue on multiple occasions.
"Of course, it's not the best way to win a match," del Potro said. "I don't like to see him suffering on [the] court today. So I'm sad for him."
With the victory, del Potro advances to a Grand Slam final for the first time since he won at Flushing Meadows in 2009.
The Argentine moves on to face two-time U.S. Open champion Djokovic, who upended No. 21 Kei Nishikori Friday night.
Djokovic won the semifinal match 6-3, 6-4, 6-2 to advance to his eighth career U.S. Open final. The Serbian lost in the 2014 U.S. Open to Nishikori, but since has defeated him in every contest between the two.
Del Potro and Djokovic square off Sunday at Arthur Ashe Stadium in New York.