The world number one joins American Bill Tilden in joint fifth on the all-time Grand Slam titles list and extends his winning run to 36 matches.
Gonzalez had his chances, missing two set points on his own serve in game 10.
But Federer hit back to dominate the tie-break and one break was enough in each of the second and third sets.
"It is just wonderful," said Federer afterwards. "I have had a great run here again this year. I am very proud to be holding this trophy again."
Among the growing list of statistics that back up the Swiss star's dominance of the game, he now becomes the first man to win a Grand Slam title without dropping a set since Bjorn Borg at the 1980 French Open.
He is also the first man to win three of the Grand Slam events on at least three occasions each.
And he is now one title away from joining Borg and Rod Laver on 11 Grand Slam tournament wins.
The 25-year-old went into the final as an overwhelming favourite after one of the great performances in beating Andy Roddick in the semi-finals.
But Gonzalez had shown exceptional form himself in seeing off James Blake, Rafael Nadal and Tommy Haas in straight sets.
And, after a slightly nervous start, it was the hard-hitting Chilean who made the first significant move, breaking Federer in game nine with a backhand pass.
The key moment of the match came in the following game when, at 40-15 and with two set points, Gonzalez could not convert.
A Federer volley saved the first and 10th seed Gonzalez missed an attempted forehand winner on the second.
The set came down to a tie-break and Federer showed his class by racing 5-0 clear, dominating the battle of the forehands and taking his first set point.
Gonzalez made 42 winners and three unforced errors in his semi-final and needed that kind of form again to trouble Federer, but it was a different story against the world number one.
In a low-key second set Federer dominated on serve, converting the only break point in game seven.
And despite an impressive recovery from Gonzalez in the third it was a similar story, with Federer breaking in game seven and sealing victory three games later with an incredible backhand pass.
"I have to congratulate Roger again, he's a great champion," said Gonzalez.
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