The throw glanced off Lowrie's glove, and as he turned his body to look for the ball, Gregor Blanco slid into the bag and appeared to spike the shortstop's ankle.
Lowrie, who leads Houston with 14 home runs, immediately dropped his glove and hopped around on one foot before falling to the infield dirt as manager Brad Mills and a team trainer rushed from the dugout. Lowrie was eventually helped off the field and replaced by Brian Bixler.
The Astros went on to lose 3-2 in 12 innings.
Information from The Associated Press was used in this report.