Jonathan Campbell notched his first career goal with less than 10 minutes to play in the first half.
After the Tar Heels earned a free kick 35 yards from goal, Cameron Brown stepped up and struck a low ball on target.
Clemson's Cody Mizell was able to get in front of the effort but the rebound skipped to a waiting Campbell who headed home the goal and put Carolina in front 1-0.
Carolina went into the break with a 6-5 shot advantage after controlling possession in the first 45 minutes.
Sophomore Mikey Lopez made a two-goal lead for the Tar Heels early into the second half thanks a tremendous individual effort.
Lopez corralled a ball in the midfield and found some open space before unleashing a shot from 30 yards out. The effort curled into the upper left 90 of the goal as Mizell was unable to get to the ball. For Lopez, it was his second goal of the year.
Clemson mounted a charge in the 63rd minute when goalkeeper Scott Goodwin came up with the save of the night.
Preston Gayton found the ball on the right side of the 18-yard box and was one-on-one with Goodwin. Gayton fired and Goodwin was able to get in front of the try. The rebound found Clemson's Paul Clowes at the top of the box.
Clowes fired the second shot just wide of the target and out for a goal kick.
The physical match saw three yellow cards and a red card issued to the Tigers in the final five minutes of action alone. Both teams combined for 30 fouls on the night as the Tar Heels fought for their fifth-straight win.
Carolina runs its conference unbeaten streak to 15 straight matches and have not lost an ACC regular season match their last 12 times out.
Up next for the Tar Heels is a visit from Davidson on Tuesday, Oct. 9 at 7 p.m. at Fetzer Field.