It was the first title in Spain for the Swiss world number one as he maintained his perfect record over his Chilean opponent in their eighth career meeting.
Gonzalez has won just two sets against the Swiss, who now owns 43 career titles and stands 82-5 on the season.
Again in the midst of another long winning streak, Federer has won his last 19 matches, including the title at the US Open and Tokyo.
It's also the third straight year the Swiss has finished in double figures in the season trophy count.
The brutally efficient victory was achieved in just one hour, 47 minutes.
"I missed 2004 here with fatigue and I was injured last year," said Federer.
"I finally made it back here and I was able to win it. It's been a fantastic week and it's a great day in my career."
Among his 43 career titles, Federer now owns a dozen from Masters Series.
There are two more opportunities for the 25 year old to improve his haul this season as he is entered to play in his home town of Basel which starts on Tuesday and in the final event of the season, the Masters at Paris beginning on October 30.
Federer and rival Rafael Nadal, who was eliminated in the quarter-finals by Czech Tomas Berdych, are the only men so far qualified for the season-ending Masters Cup in Shanghai.
Gonzalez, who has won just two sets in eight losses to Federer, stands provisional ninth as he travels to Basel, where he is defending the title.