However, the All-Star second baseman was in the lineup for Sunday's finale with the Phillies.
DeFrancesco said the decision hinged on shortstop Jed Lowrie's ability to play.
After Saturday's game, Lowrie told DeFrancesco he was feeling some soreness in his right leg. Lowrie missed nearly two months with a nerve injury in the leg. Tyler Greene started at shortstop on Sunday.
DeFrancesco hinted that Greene would replace Altuve at second base on Tuesday in St. Louis.
"I kind of like the combination of Greene with Jed out there," DeFrancesco said. "You look at the numbers -- there's 24 homers between the two, so maybe that can help us get a little more punch on the road."
First baseman Brett Wallace also wasn't in the lineup on Sunday. Since DeFrancesco took over as manager on Aug. 19, Wallace had started and batted third in 24 of 25 games.
DeFrancesco said Wallace hyperextended his elbow recently, and it was affecting him at the plate. Wallace hit .100 (2-for-20) in the first five games of the Astros' homestand.
The injury didn't sound too major, though.
"You do need breather days around here," DeFrancesco said. "Just a mental break, sometimes, to clear your mind."