Matt Jones was undergoing surgery around noon on Monday.
The injury occurred in the first half on Saturday when Jones was tackled in front of the Florida bench. The hit came from the back of his knee, awkwardly wrapping him up before he came off the field. He later showed up in street clothes on the Florida bench for the second half.
The injury forces the Gators to reassess in the backfield.
Mark Herndon, who earned a scholarship this fall, will serve as the third running back. Valdez Showers will continue to be involved, although Muschamp noted he wasn't capable of handling a full load at running back.
"We'll go from there with those guys," Muschamp said.
Jones ends his sophomore season with 79 carries for 339 yards and two touchdowns. He was averaging 67.8 yards per game and 4.3 yards per carry.
"I hate it for Matt," Muschamp said. "He's a great young man. To go through what he has been through this fall, to have this setback, it's disheartening."
The Gators have now lost five starters to injury this season, including quarterback Jeff Driskel (fibula), offensive tackle Chaz Green (shoulder), wide receiver/kickoff returner Andre Debose (knee), defensive tackle Dominique Easley (knee) and Jones.