Left-hander Mike O'Connor has been promoted from Triple-A Buffalo.
Beato said that he began to feel pain in his arm while throwing on Tuesday. He felt fine after the outing Sunday night in Philadelphia, but assumed that the injury was related to that appearance.
"It's terrible, I want to be out there on the field," said Beato, who will remain in New York to rehabilitate the injury.
Beato has not allowed an earned run in 17 innings, the second-longest streak to open a Mets career in franchise history. Jack DiLauro did not allow an earned run for 17 2/3 innings to open his major league career in 1969.
Manager Terry Collins said that the team wouldn't place any added restrictions upon Beato when he returns. He praised pitching coach Dan Warthen for being cautious when it comes to the health of his staff.
Beato underwent Tommy John surgery during his stint at Xaverian High School in Brooklyn. Mets team doctor David Altchek performed the surgery.
"We are in the big leagues. We don't sometimes have the option to start protecting people," Collins said. "Will we watch him? Yea we'll try to be careful with him. But we've only got seven guys down there, so somebody's got to pitch."
O'Connor, 30, last appeared in the majors with the Washington Nationals in 2008. He was 2-1 with a 3.31 ERA in 16 1/3 innings spanning 10 relief appearances with Triple-A Buffalo this season.
"We called down there and he was the guy pitching the best out of the bullpen, which allows us to have a second lefty," Collins said.
Adam Rubin covers the Mets for ESPNNewYork.com. ESPNNewYork.com's Ian Begley contributed to this report.