Gonzalez, Olympic gold medallist in the men's doubles last year and defending champion here, saved four match points in the final game before Gaudio won 6-3 6-4 in one hour 37 minutes to claim his first tournament since Roland Garros last June.
The Argentine clay court specialist, who kept his composure despite some often rowdy crowd behaviour, broke in the eighth game as he took the first set in 44 minutes.
Big-hitting Gonzalez, who was attempting to win the tournament for the third time, made a good start to the second set as he broke in the fourth game and took a 4-1 lead.
However, the Chilean second seed remained prone to unforced errors, committing 26 in the match, and Gaudio took advantage as he broke in the seventh and ninth games to go 5-4 ahead.
Gaudio, who lost four ATP finals last year, then seemed to suffer from another bout of nerves in the last game.
Gonzalez saved the first two match points with powerful returns off a second serve before Gaudio double-faulted on the next match point.
Gonzalez saved the fourth with another return before Gaudio finally wrapped up the title at the fifth attempt.
