Lowrie, who was hurt in a collision at second base on Saturday against the Giants, was set to return to Houston for a further evaluation that would determine how long he might be out.
The Astros said Lowrie has a sprained right ankle and an injury to the peroneal nerve in his right knee.
"We'll let the doctors look at him and we'll know more then," manager Brad Mills said.
Marwin Gonzalez was activated from the disabled list to take Lowrie's spot on the field and on the roster. Mills said Gonzalez will get the bulk of the playing time at shortstop.
Lowrie was still walking with the aid of crutches when he arrived at the ballpark on Sunday. He reported to trainers that he felt "a little bit better, but not a whole lot," Mills said.
Lowrie was trying to make a force at second in the third inning on Saturday night. He was stretching to take a throw from second baseman Jose Altuve when Giants outfielder Gregor Blanco slid into Lowrie's leg. Blanco's foot pinned Lowrie's leg, and he injured his ankle and knee stretching.
Lowrie has 14 homers, second most among National League shortstops to Washington's Ian Desmond, who has 17. His .343 on-base percentage is tops among NL shortstops.
Gonzalez had been on the disabled list because of a bruised right heel. He was hitting .333 at Triple-A Oklahoma City on his rehab assignment.
Brian Bixler, who replaced Lowrie when he left Saturday's game, may also get some time at shortstop, Mills said.