The Spaniard, bidding for a ninth title at the claycourt tournament having reclaimed his Monte Carlo crown last week, cruised through the first set against the Italian but he went off the boil in the second.
Fognini, who beat Nadal in the tournament last year and knocked him out of the U.S. Open, hit back with two breaks after trailing 0-2 in the second set and served to send the match into a decider.
Showman Fognini saved three match points from 0-40 at 5-6, one with an outrageous drop shot, before succumbing in the tiebreak.
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Left-hander Nadal, eyeing a 10th French Open title next month, will face Andrey Kuznetsov or Philipp Kohlschreiber in the semi-finals.
In the other half Japanese second seed Kei Nishikori, bidding to defend the title, beat Alexandr Dolgopolov in straight sets and will play unpredictable Frenchman Benoit Paire for a place in the final.
(Reporting by Martyn Herman, editing by Ed Osmond)
