The world number two had few problems beating Chilean Gonzalez, who struggled to get back into the final after making an error-riddled start.
The win gave Nadal his 13th consecutive claycourt title and extended his winning streak on the surface to 77 matches.
The Spaniard also equalled Thomas Muster's professional-era record of three Rome victories, though the Austrian won his over a period of seven years, in 1990, 1995 and 1996.
"It's incredible. To win here for a third time is a dream," Nadal said at the courtside, before admitting the match had been easier than he expected.
"Fernando made far more mistakes than usual and I took advantage of that."
Gonzalez had defeated Nadal in straight sets on the way to reaching the final of the Australian Open in January.
This time, however, the 26-year-old Chilean appeared out of sorts.
The metronomic groundstrokes he had used to sweep aside Italian wildcard Filippo Volandri in the semi-finals deserted him.
Instead he made a succession of unforced errors, gifting Nadal breaks in the first and fifth games to lose the first set in just over half an hour.
He could not find his rhythm at the start of the second set either. A netted backhand, a shot that flew wildly off the frame of his racquet, and a forehand into the tramlines gave Nadal a break in the opening game.
When Gonzalez created his first breakpoint of the match in the following game, Nadal responded with a big first serve that the Chilean put over the baseline.
Nadal broke again in the third game and Gonzalez managed to pull a break back, but in the seventh game Nadal chased down a dropshot to flick a winner past his rival and restore his two-break lead, then served out for the match.
"It's very difficult to play against Rafael. I always thought I would have some chances, but he played good tennis -- much better than me today," said Gonzalez.