Jesus Feliciano got the start in left field.
Bay was injured while beating out a single in the second inning of the Mets' 8-4 victory at Cleveland on Wednesday. He collided with Indians first baseman Andy Marte and was knocked to the ground. Bay got up limping but stayed in the game. He was removed in the sixth.
Bay attempted to talk manager Jerry Manuel into letting him play in the series finale against the Indians.
"I tried, but it was a losing battle," Bay said. "It made sense to give it a day. It's a little tight. It's not life or death. There's a little knot in there."
The Mets gave some thought to using Bay as the designated hitter.
"We talked about it, but that actually would have been a worse idea," Bay said. "You're sitting around for a while and then running. You might have to sit for an hour and then sprint."
Bay was available to pinch-hit and plans on being in the lineup Friday night when the Mets open a three-game series at Yankee Stadium.
"We thought it might be best to make sure we get it cleared up before we put him back out there," Manuel said.
Bay is batting .283 with four homers and 27 RBIs in 64 games this season.
Information from The Associated Press was used in this report.