It was a remarkable performance by the 18-year-old fifth seed, who fought back from 3-0 down in the deciding set despite needing treatment on a badly bruised and blistered racquet hand.
Nadal, who triumphed in Monte Carlo and in Barcelona before arriving in the Italian capital, has won five of his seven claycourt tournaments this season.
His 17-match winning streak makes him one of the favourites for the French Open, which starts in Paris on May 23.
Nadal's win also extended Spain's stranglehold on the Rome title, following victories by Juan Carlos Ferrero in 2001, Felix Mantilla in 2003 and Carlos Moya 12 months ago.
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