The Argentine, 25, displayed majestic power and Nadal was unable to gain a single break as a high-class contest ended in an hour and 46 minutes.
Del Potro will play defending champion Novak Djokovic, who beat seventh seed Jo-Wilfried Tsonga 6-2 7-5.
"I played so solid all the time, hitting the ball so hard," said Del Potro, who also secured his place at next month's World Tour Finals in London.
"I saw Rafa playing very far off the baseline, which is good for my game, for my serve, and confidence. That's the way to beat this guy.
"I didn't make too many aces but that's what I need against Djokovic. I need to win easy points with my serves.
"Hopefully, my forehands and backhands work like today in the final. I'll be aggressive like today."
A rueful Nadal, who could not convert any of his six break-point opportunities, conceded Del Potro deserved victory.
"Very few times I have played against a player with a level like today," said the Spaniard. "At the end I played against a player who served 80% of first serves, who hit every ball as hard as he can I think, and with no mistakes."