Padres manager Bud Black said the combination of a day game after a night game and the fact that Gonzalez aggravated his right shoulder on Monday were the reasons he decided to give Gonzalez a breather with Rockies' left-handed starter Jeff Francis on the mound.
Gonzalez had started 74 of the Padres' 77 games at first base entering Wednesday.
"[We'll] let [the shoulder] quiet down against a lefty, where we have an opportunity to get our right-handed bats in there," Black said.
Oscar Salazar made his second start of the season at first base in Gonzalez's place. Salazar also started at first last week against the Rays, when Gonzalez served as the designated hitter.
Gonzalez being omitted from the starting lineup was one of a few tweaks for the Padres on Wednesday, as regulars David Eckstein and Tony Gwynn also got the day off. Jerry Hairston Jr. started at second base and hit leadoff and Chris Denorfia got the start in center field and hit in the No. 2 hole.