"I have been working so hard to enjoy moments like this," Nadal said. "The fact that I'm playing at home is always even more special. I'm very happy and I feel lucky to enjoy this again."
Playing with the kind of authority that once made him almost unplayable on European clay, Nadal looked poised for a comfortable victory when he led 4-1 in the second set but Nishikori broke back to make Nadal dig deep.
The Spaniard would not be denied, though, sealing victory after two hours when Nishikori slapped a forehand into the net.
"It was a very close match," Nadal said. "There were a lot of chances for both of us but I think I have been solid."
Nadal, who will target a 10th French Open title next month, had not won back-to-back titles since 2013.
He and former Argentine great Vilas have both won 49 claycourt titles and Nadal will be confident of edging ahead when he moves on to Madrid and Rome before Roland Garros.
(Reporting by Martyn Herman, editing by Ed Osmond and Ken Ferris)
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