The Marlins didn't give a reason but said they expected Alfaro to return this season.
The Atlanta Braves were without their top two catchers, Tyler Flowers and Travis d'Arnaud, for their opening game Friday at the New York Mets after both players showed symptoms of the coronavirus. There has been concern that catchers are especially vulnerable to the virus because they're in close proximity to batters and the plate umpire.
The Marlins learned Friday morning Alfaro would be unavailable, manager Don Mattingly said.
"We knew we were going to have to be ready for anything," Mattingly said. "We still plan on having him back, and still plan on big things for him."
Alfaro batted .262 with 18 homers and 57 RBIs last year in his first season with the Marlins.
Miami newcomer Francisco Cervilli was in the lineup in place of Alfaro. The Marlins selected the contract of infielder Sean Rodriguez from their alternate training site.