Manager Dusty Baker said doctors weren't able to find any cause of the breathing issues. Alvarez was at the ballpark but under a concussion-like protocol in which the team was monitoring his every move.
Baker said Alvarez could return to the lineup for the finale of the three-game series Sunday.
"He's better," Baker said. "We've still got to watch him. He's under what's similar to a concussion protocol, where you've got to watch him. You don't want him to maybe fall out. They couldn't find anything, but that doesn't mean nothing's wrong."
Baker called it a frightening situation but added he was somewhat relieved that one of the game's most feared hitters was apparently not stricken with a serious medical problem.
"We're just going to wait today," the manager added. "We'll see how he is tomorrow. He'll probably DH if he's feeling all right."
Alvarez is batting .295 with 31 homers and 77 RBIs for the AL West-leading Astros, who are seeking their fourth World Series appearance in six years.
They are in Atlanta for a rematch of last year's Series, won by the Braves.
Alvarez departed Friday night's 6-2 loss to Atlanta under his own power with two outs in the bottom of the fifth inning. There was a pause in the action when Braves rookie Vaughn Grissom fouled a ball off his foot and was being tended to by a trainer.
Baker said Alvarez started having some breathing issues while running the bases, and the condition was exacerbated by in-game fireworks.
Alvarez had hoped to make it through the inning but decided to come off when Grissom was shaken up.
Alvarez was transported to an Atlanta hospital to undergo testing, but doctors weren't able to pinpoint a cause.
"It's better to know if there's nothing wrong," Baker said. "Those doctors are great, but sometimes it's a guess."