Michaels, the oldest player on a team that features 16 rookies, made his 29th start of the season and went 0-for-1 before being forced to leave the game with a displaced fracture of the fourth metacarpal of his left hand. Normal recovery time is approximately six weeks.
Michaels, 35, was injured when he made a diving catch to rob Ryan Howard of a hit in the second inning and rolled his glove hand under his body.
"I couldn't close my glove," he said.
The injury capped what was a frustrating season for Michaels, who batted .199 with two homers and 10 RBIs in a part-time role this year. He was 8-for-45 (.178) as a pinch-hitter.
"It's just the exclamation point," Michaels said. "It stinks."
The injury leaves the Astros with five healthy outfielders, but manager Brad Mills said the team would be able to manage in the final two weeks of the season.