The fifth-ranked del Potro overpowered Nadal with his deep, punishing groundstrokes, breaking the Spaniard twice at the start of the match to race out to a 4-0 lead.
The Argentine broke Nadal again to start the second set, and saved all six break points he faced to get his first victory over the Spaniard in four years.
Del Potro will try to win his first Masters title on Sunday against top-seeded Novak Djokovic, who defeated Jo-Wilfried Tsonga in the other semifinal, 6-2, 7-5.
Nadal was playing his first tournament since regaining the No. 1 ranking from Djokovic on Monday.
Djokovic put himself in position to win back-to-back titles in China for the second straight year.
The Serb extended his winning streak in China to 19 straight matches dating to last year when he won the China Open in Beijing and then Shanghai.
He successfully defended his China Open title last week and will try to do the same in Shanghai on Sunday.
"I've always been coming out in China and making some really, really good results, winning trophies,'' Djokovic said. "It's very positive because most of the people would think after the fourth Grand Slam of the year is over, that somehow the season is finished in the minds of maybe people who are not following consistently the tennis season.''
Djokovic raced out to a 3-0 lead after only seven minutes against Tsonga, who came out looking flat and misfiring wildly at times on his groundstrokes and volleys.
However, Djokovic then lost his temper in the second set when serving at 4-2, yelling angrily at chair umpire Ali Nili after two disputed calls.
Tsonga twice challenged late calls that went against him -- and both times the Hawk-Eye camera replay showed the balls had clipped the line. The umpire awarded both points to the Frenchman, prompting a furious reaction from Djokovic who thought the points should have been replayed.
"Twice I was on the ball, twice you take the point away from me,'' Djokovic yelled. "Focus!''
Tsonga managed to break the rattled Serb to get back on serve at 4-3, but his comeback was short-lived as another error-strewn game allowed Djokovic to break him at 6-5 to close out the match.
"When you're on the tennis court, it feels like an arena,'' Djokovic said about his outburst. "You're fighting. It's emotional. It's intense. It's normal. It's not the first nor the last time.''
Tsonga, who missed several months this year with a knee injury, still boosted his chances of reaching the season-ending ATP finals, moving into position to claim the last spot in the eight-man field for the tournament in London, with three weeks left to play in the season.
"I have to play if I want to go,'' Tsonga said. "I just have to play and try to win as much as possible.''