Rodriguez was replaced in the lineup and at third base by Eric Chavez, who went 0 for 3 with two strikeouts as the Yanks topped the Orioles, 3-1, to advance to the AL Championship Series against the Detroit Tigers.
Rodriguez said he wasn't happy about not being in the lineup while talking to reporters before the game but noted the team was the first priority.
"Obviously, I'm not happy and, you know, I was disappointed. You want to be in there in the worst way," Rodriguez said. "But I keep telling you guys, this is not a story about one person; this is about a team. We have some unfinished business. Our objective is to win one game and keep this thing moving."
Girardi had pinch hit for Rodriguez late in the previous two games. In Game 3, Raul Ibanez hit a game-tying home run in the ninth inning and another homer in the 12th to win it.
"The man has a lot of pride and the man has accomplished a lot in his career," Girardi said of Rodriguez. "I'm sure it's not easy. I mean, imagine if you're in his shoes? Everyone wants to be in it. I always wanted to play, too. And I understood. It's something he'll have to deal with."
Rodriguez is 2 for 16 with nine strikeouts in the series. A career .300 hitter, Rodriguez went 2 for 18 in last year's playoffs.
Rodriguez, of course, isn't the only Yankee struggling. But he said he does not feel singled out by Girardi's move.
"No. It is what it is. You don't worry about that. I can't control that," Rodriguez said. "The only thing I can do is go out and try to have quality at-bats and help the team win."
Girardi admitted the idea that he would one day bench Rodriguez would have been unfathomable not long ago.
"I would have bet against that," Girardi said.
Even after being pinch hit for the past two games, Rodriguez said after Game 4 that he "absolutely" thought he would be starting at third in the next game.
Girardi said he made the decision to bench Rodriguez at 1 p.m. ET and contacted the slugger, who wasn't at the park yet. Girardi said Rodriguez told him he would be ready if called upon.
Girardi mentioned possibly pinch-hitting Rodriguez against a lefty.
"As you know, with 27 outs, a lot can happen. I'll be ready from the first inning on," said Rodriguez, who did not end up entering the game as a pinch hitter -- or in any other capacity.
Before the game, Rodriguez acknowleged having mixed feelings about Girardi's decision.
"It's never about Joe. I always have to look in the mirror and do what I can do to do the best I can. Don't assume that you've heard the last from us, or me," he said.
"We're ready to go tonight. We've got to win one game and I'm a part of this team. And I'm ready to roll and I'll be ready."
Information from ESPNNewYork.com's Wallace Matthews and Ian Begley was used in this report.