Altuve and Hernandez were chasing a popup in right field and stayed down after the collision.
The pair appeared to avoid serious injury and was in Houston's clubhouse following the game.
"Nasty collision, both guys going 100 percent after the ball,'' manager A.J. Hinch said. "That's a scary scene. It was an all-around good game, except for the collision.''
Altuve and Hernandez crashed into each other chasing a popup in right field and stayed down for a while. Altuve appeared to get hit near his chin by Hernandez's arm, but he walked off the field under his own power. Hernandez, called up from the minors before the game, was carted off the field with a left leg contusion.
Hinch said Altuve's left shoulder got banged up and a decision will be made Wednesday whether he'll play in the second game of the series.
"He's gotten checked out by the doctors, he didn't have a concussion, he was never out,'' Hinch said. "We'll see how he wakes up tomorrow. He'll probably feel like he was in a car wreck of some sort.''
Altuve, last season's AL batting champion, plans on being in the lineup.
"I'm a little sore, but I'm feeling better,'' he said. "I think we still have to wait until tomorrow, but I have a good chance to play.''
Hernandez could miss some time, and his injury is another setback for Houston's outfield. George Springer (strained left hamstring) didn't start for the second straight game but came in after the collision, and Jake Marisnick (concussion) is out.
The Associated Press contributed to this report.