Nick Punto, who had been playing third in place of Middlebrooks, had to take Pedroia's spot at second.
Gomez is mainly a first baseman. He hadn't played third base in the Minor Leagues since 2009. As a third baseman in the Minors, Gomez has 31 errors in 71 games.
With sinkerballer Aaron Cook pitching for the Red Sox on Wednesday, this was hardly an ideal situation.
"It is what it is," said Valentine. "What are we going to do, you know?"
Middlebrooks was on the bench for all three games in Oakland, and the Red Sox still aren't sure if they will have to put him on the disabled list.
The club hopes Middlebrooks can play at some point this weekend, when the Yankees come to town for a four-game series. By placing Middlebrooks on the disabled list, Boston would be without him until July 15.