"This is where I'm kind of kicking myself a little bit," Francona said. "We might have gone a little too far, too much, too fast. I didn't want to do that, but we probably did. We'll give him tonight and probably tomorrow to allow him to bounce back like we want him to.
"It's hard to do that ... just want to make sure he's not just 'playing two, sitting two' and not being the kind of hitter he can be. I don't think he's thrilled with it."
Brantley seemed to be working back into form, cranking out seven hits and driving in six runs over five games against Detroit and Kansas City. The Indians left fielder went 0-for-4 on Monday night in a 7-1 loss to the Astros.
Brantley didn't take batting practice before Tuesday's game.
The eighth-year veteran missed the first three weeks of the season due to the November procedure, and he has just two extra-base hits and no home runs in 43 plate appearances.
Francona said the decision was a mix of precaution and a reaction to Brantley's shoulder getting sore after playing six games in seven days.
"Probably more the bouncing back, the recovery is probably the biggest thing," Francona said. "I'm sure everyone who has had surgery probably had some soreness after.
"We watch these guys pretty careful, and you kind of get to know their mannerisms, so we sat and talked for a bit, and it just made sense."
Jose Ramirez started Tuesday night's game in left field.
Chris Abshire is a contributor to MLB.com based in Houston. This story was not subject to the approval of Major League Baseball or its clubs.