Harris replaces fourth-year junior Jeff Driskel, who has struggled mightily in the Gators' last four games.
"[Harris] is getting all the reps right now," Muschamp said, "and Jeff is certainly going to have a role in that game."
Florida has a bye week before facing No. 9 Georgia (6-1, 4-1 SEC) on Nov. 1 in Jacksonville, Florida.
The Gators (3-3, 2-3 SEC) are coming off two straight home losses, including an ugly 42-13 homecoming defeat to Missouri on Saturday that saw fans boo Driskel and chant "Fire Muschamp" before flocking to the exits in the third quarter.
Driskel has had 12 turnovers in his last 14 quarters, while Harris has sparked the offense with extended playing time in the fourth quarters of the Tennessee and Missouri games.
Harris was suspended the week after leading Florida to a come-from-behind 10-9 victory at Tennessee after police investigated an accusation of sexual battery from another UF student. Harris was reinstated five days later when the accuser withdrew her complaint.
After sitting in the coaches' booth for the LSU game on Oct. 11, Harris returned to the field against Missouri and was 8-of-12 passing for 98 yards with a touchdown and an interception. He also ran for a touchdown and lost a fumble on a first-quarter sack.
"You saw what he did late in the game," Muschamp said Wednesday. "He has a knack for making plays and making some good things happen for our football team. We've struggled with production at the quarterback position, and that's been an issue for us along with others. Been a huge issue for us.
"He's got a much better understanding as we continue to move forward. We've got an open week now where he's getting a bunch of reps. Jeff's still going to have a role on our football team as a quarterback. Right now we feel like that was the best move moving forward."