Manzella injured the finger during Monday's game against the Giants, but didn't realize how serious it was until an X-ray revealed the fracture on Tuesday.
The Astros recalled Oswaldo Navarro from Triple-A Round Rock to take Manzella's spot on the roster. Manager Brad Mills says Geoff Blum and Navarro will fill in at shortstop while Manzella is out.
Manzella was hitting .212 with one home run and 16 RBIs this season.
Also on Wednesday, catcher Kevin Cash and right-hander Casey Daigle cleared waivers and accepted their assignments to Round Rock. Outfielder Cory Sullivan also cleared waivers, but elected free agency.