Herrera, who legged out an infield hit to third on the play, came out of the game and was replaced by pinch-runner Ruben Tejada, who stayed in the game defensively.
Mets manager Terry Collins doesn't know how long Herrera will be out beyond saying that he will not be available for Sunday's series finale against Atlanta.
"It's too early to tell but he won't be in there tomorrow. I can assure you that," said Collins. "We'll see how he is in a couple of days but you have to be very careful with any of those leg injuries. It's too bad."
The 20-year-old Herrera had been one of the Mets' hitting stars Saturday, with two hits in three trips to the plate, including a two-run homer in the top of the second inning off Braves pitcher David Hale that expanded New York's lead to 3-0. It was his third homer since being called up Aug. 29.
Herrera, who was 3-for-6 in the series, had come back strong following a three-day respite by Collins. Acquired from Pittsburgh at last year's Trade Deadline along with reliever Vic Black for Marlon Byrd, John Buck and cash, the Cartagena, Colombia, native, showed plenty in his first full season in the Mets' organization, tearing up Class A Advanced St. Lucie and Double-A Binghamton, batting a combined .323 with 13 homers and 71 RBIs in 128 games.
He also showed he could hit at the Major League level, batting .265 over his first nine games, with a triple, two homers, seven RBIs, two multi-hit games, including a three-hit game, and a pair of three-game hitting streaks. But he cooled over the next seven, going 1-for-19 (.053), resulting in Collins giving him the three days off.
Herrera is hopeful he won't be out too long.
"I'm going to hope everything will be OK," he said. "I just wants to play. So I'm just going to see how it feels tomorrow."
Regardless, Collins is sure Mets fans have only seen the beginning of what he can do.
"I like a lot about Dilson Herrera," he said. "He's going to be a very good player. It's just a matter of him getting some games under his belt and getting some experience at the higher levels. But I like him a lot. I like the way he swings the bat, he's gotten better defensively and I told [third-base coach Tim Teufel], 'A little brief time in Spring Training on Field 3, he'll be a lot better.'"