Eric Chavez, 3-for-6 with a homer and two strikeouts, won out over Raul Ibañez, who was 2-for-6 with a homer and one strikeout.
Chavez started at third and hit ninth.
"There's other things I look at, the types of pitches he hits," Girardi said. "And you look at Chavy, he's 3-for-6 and he's squared up four balls on this guy. I know it's a small sample but obviously he's seen him and sees the ball [well]."
Ibañez has had his share of big hits this season and Girardi likes the option of the 40-year-old as a pinch hitter.
"He's been a really big pinch hitter for us, and I like having that," Girardi said. "That's not the reason I didn't start him. It's just I looked at Chavy -- and Raul's at-bats were pretty good off this guy [Gonzalez], too -- but Chavy's at-bats were really good, so I decided to go that way."
Mariano Rivera, who hasn't pitched since May 3 when he hurt his right knee in batting practice in Kansas City, threw out the ceremonial first pitch Wednesday night.