The newly-crowned world number one went down 6-2 6-4 on Saturday as Del Potro booked his place at next month's ATP World Tour Finals.
The Argentine will now meet defending champion Novak Djokovic in Sunday's final.
"He played amazing," Nadal told the ATP's official website. "I just congratulate him. Very few times I play against a player with a level like today."
Nadal will return to action at the end of month when he takes part at the Swiss Indoors.