The Marlins on Saturday also recalled outfielder Bryan Petersen from Triple-A New Orleans, providing a left-handed bat off the bench.
With Baker on the disabled list for the first time in his big league career, Ronny Paulino projects to get the majority of the work behind the plate. On Saturday, however, Brett Hayes was in the lineup, making his first big league start at Sun Life Stadium. Paulino will start on Sunday in the series finale.
"We're a team that's trying to make the playoffs," said Baker, who is batting .218 after 78 at-bats. "We can't run a guy out there who is at 50 percent. It's a fine line. You want to be a tough guy, but at the same time, I've got 24 other people to think about."
Baker had an MRI on Friday morning, which revealed the flexor muscle strain. The encouraging news is he has no ligament damage.
"It showed no ligament damage, which is what we were worried about," Baker said. "I was really happy about that."
The earliest Baker can be reinstated is May 28, when the Marlins are home facing the Phillies. That date, however, may not be realistic for a return. At least initially, Baker will rest, and eventually, he likely will play rehab-assignment games before coming back.
The Marlins on Thursday promoted Hayes from Triple-A New Orleans, giving catching depth if Baker's arm didn't improve.
Manager Fredi Gonzalez said the initial plan was for Baker to remain active for the four-game series with New York.
"We thought we could make it through this weekend without playing him," Gonzalez said. "The doctor said he needs rest."
Baker encountered some arm soreness early in Spring Training, and it didn't go away. The catcher appeared in eight Grapefruit League games and had 21 at-bats.
Baker said his forearm area began acting up in the cold weather of the April 23-25 series at Colorado, where it snowed one day.
"I just know that since Colorado, when we got out of that cold weather, it's had an effect," said Baker, who hasn't hit a home run all season.
In watching video of his at-bats, Gonzalez and hitting coach Jim Presley could tell Baker wasn't himself.
"Believe me, you want them to play," Gonzalez said. "You don't want guys, every time they foul a ball off, they're coming out of the lineup. Then you see, this guy is not the same guy. You've got to take that out of their hands and do what's best for him, No. 1, and for the team."