Boone, 36, has been on a Minor League rehab assignment since Aug. 10 and had 15 at-bats for Double-A Corpus Christi before moving to Triple-A Round Rock, where he was 0-for-4 in two games.
The Astros open a three-game series Friday against the D-backs in Phoenix, where Boone lives.
Boone signed with the Astros over the offseason with hopes of platooning with Geoff Blum, but he underwent surgery to repair a congenital defect in his aortic valve in March.
It's not known how much playing time Boone will get, but the fact he will return to the field is a major accomplishment.
Brian McTaggart is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.