The Tar Heels (54-8) led 5-0 in the sixth before the third-seeded Tigers (30-29) rallied with three runs in the eighth off Emanuel. Two of those came on a bases-loaded single by Kurt Wentz, helping the Tigers pull within 7-5 before UNC reliever Trent Thornton forced Brendan Butler to fly out to end the inning.
UNC added an insurance run on Skye Bolt's sacrifice fly in the ninth, then Thornton ended it by forcing Hunter Bennett to fly out.
Emanuel (11-3) allowed nine hits in 7 2-3 innings, while Towson's Brandon Gonnella (4-5) allowed 11 hits and seven runs in 7 2-3 innings.
Towson meets Florida Atlantic in an elimination game Sunday.