Tank Norman picked off a Johnson pass and returned it 28 yards into the end zone to pull Charlotte to 10-7 with 10:58 left. The Owls sealed it when Rose scored with 1:28 remaining.
Kalif Phillips led the 49ers (2-2, 1-1) with 165 yards rushing on 29 carries.
It was Charlotte's first-ever Conference USA home game.
AP College Football website: www.collegefootball.ap.org