The Hurricanes never trailed as they built an 11-point halftime lead and outscored the 49ers 14-6 in the opening 5:27 of the second half. Rion Brown's 3-pointer with 14:33 remaining ended the spurt and gave Miami a 47-28 advantage.
Scott's three-point play with 12:48 remaining gave the Hurricanes (6-1) their first 20-point lead at 50-30.
The loss snapped a nine-game winning streak at the start of the season for the 49ers (9-1).
Charlotte got to within 52-39 on Victor Nickerson's 3-pointer with 9:46 left. But Miami, which played its first game in 13 days, ran off 14 unanswered points in the next 5:26.
Kadji's two free throws with 4:20 remaining capped the run and gave the Hurricanes a 66-39 lead.
Chris Braswell's layup with 3:41 remaining ended a scoreless drought of 6:05 for the 49ers. Braswell finished with 13 points and Willie Clayton scored 11 for Charlotte, which shot 31.7 percent (20 of 63) for the game.
Kadji and Shane Larkin hit 3-pointers to help the Hurricanes open a 12-2 lead in the first 3:47. Rion Brown converted 1 of 2 free throws with 11:52 remaining in the half as the Hurricanes increased their advantage to 21-8.
Miami maintained a double-digit lead most of the first half and had its largest advantage at 33-16 on Scott's driving layup with 4:11 remaining.
The 49ers kept Miami scoreless the rest of the half and scored six unanswered points. Braswell's two free throws with 47 seconds remaining reduced the Hurricanes' lead to 33-22 at halftime.
Charlotte had a chance to cut Miami's first-half lead under double figures but DeMario Mayfield turned the ball over driving to the basket with 18 seconds remaining and Darion Clark's layup attempt bounced off the rim with 13 seconds left.
Miami guard Bishop Daniels left the team, Miami coach Jim Larranaga said. A redshirt freshman from Raleigh, N.C., Daniels averaged 5.0 points while playing in three games this season.