Henman, 31, showed considerable class against the Spanish teenager, but he lacked consistency and was ultimately overpowered even though he held the advantage early in both sets.
Henman was unable to convert three break points in the second game and two more after Nadal had broken to lead 3-2 with a return off a second serve.
The French Open champion led 5-3 and held four set points on Henman's serve. Henman eventually held with an ace and a double-fault then allowed Henman to level at 5-5.
After a tiebreak in which Henman managed to earn just one point Nadal had to resist three break points at 1-1.
He then broke Henman to love with a forehand winner that grazed the sideline.
After holding to love, Nadal broke for 5-1 when Henman netted a forehand and Nadal closed out the match with his ninth ace.
Russia's Mikhail Youzhny reached his first semi-final of the year and a possible meeting with world number one Roger Federer when he overwhelmed Olivier Rochus of Belgium 6-3, 6-1.
