Boone has been playing in the minor leagues since Aug. 10, going 3 for 15 with one RBI for Double-A Corpus Christi before moving to Triple-A Round Rock where he was 0 for 4 in two games.
Astros manager Cecil Cooper said Boone is healthy, but his timing is off.
Cooper said he hadn't thought about how Boone would be used the final month.
The 36-year-old Boone had an operation in late March because of a congenital defect in his aortic valve. He signed with the Astros in the offseason.