Springer has been dealing with a strained left quad that has kept him out since July 19. He did a minor league stint in August and had been working out with the team for the past month trying to get healthy, but is not yet 100 percent.
"We're going to shut him down and he's going to take batting practice and rehab when the season's over, and he's going to leave here healthy. And when he comes to Spring Training, he's going to be ready to go," said Astros interim manager Tom Lawless.
Lawless said they felt shutting down Springer was "the best thing for the organization."
Springer had a .231 batting average with 20 home runs and 51 RBI in 78 games this season. The 24-year-old was named the American League Rookie of the Month for May.
Houston is 67-83 and in fourth place in the AL West.
- Molly Geary