The 35-year-old Brantley, who hasn't appeared in a big league game since June 26, underwent arthroscopic labral repair. He hit .288 with five homers and 26 RBIs in 64 games in the final season of a $32 million, two-year contract.
"There were a lot of different avenues that were taken to try to get Michael back on the field in time for the end of the season,'' general manager James Click said Friday, "and ultimately, after consultation with our trainers and doctors, we ... came to the conclusion that this was the right path for him long-term for his health.''
The loss of the sweet-swinging Brantley is a big blow for AL West-leading Houston (72-41), which is 11 games ahead of the Seattle Mariners entering Friday's games. The five-time All-Star is a .298 hitter with 127 homers and 713 RBIs in 1,430 regular-season games.
Brantley also has enjoyed postseason success, batting .319 with nine RBIs during the Astros' run to the World Series last year.
"He tried hard to get back,'' Astros manager Dusty Baker said. "He got a number of opinions, he got a couple of procedural things -- it just didn't work. Michael's a big part of this club, not only on the field, but in the clubhouse and dugout and on the planes. He's not called 'Uncle Mike' for nothing.
"He wants to come around and be a part of this club as much as he can because a lot of guys depend on him. A lot of guys go to him for advice, and I feel very confident in whatever Michael gives them. So, we'll miss him, big time."
Trey Mancini, who was acquired from Baltimore as part of a three-team trade Aug. 1, also could be an option.
"Trey will be out there working on the nuances of playing left field here in Minute Maid Park," Click said. "And that's part of the reason that we acquired Trey, was that we felt like he could go out there in the corner outfield and help us out. So I'm optimistic that that's something that we will be able to see over the next couple of months.''