Manager Alex Cora confirmed the decision to media ahead of Thursday's series finale against the Guardians.
Verdugo slowed up between first and second base on a chopper by Masataka Yoshida with two outs in the top of the seventh inning and was easily thrown out at second with Boston trailing 5-2. Cora removed him from the game before the Red Sox took the field for the eighth.
"There was a play in the seventh inning that I didn't like," Cora told reporters. "I don't know if people noticed it. ... We just felt like in that play, his reaction wasn't a great one. Obviously not busting his behind to second. I don't know if he's out or safe but I didn't like it.
"One of the things with Dugie as a player this year, there's not too many things we can question. Defensively, he's one of the best in the big leagues. Offensively, he's been solid. Even baserunning, which is one of the things he needed to get better (at), he's doing a good job. But obviously where we're at, I'm not using him as an example because we have to be better in a lot of aspects. But yesterday, I felt like ... that's not acceptable and he knows it. So I took him out of the game and then today he is not starting."
Rob Refsnyder was in right field in place of Verdugo for Thursday night's game.
Cora indicated that Verdugo will be back in the lineup for Friday night's series opener against the Yankees in New York.
Verdugo is hitting .286 with five home runs and 24 RBIs for the Red Sox.