The Tar Heels (41-17) will face the winner of Saturday's second semifinal between North Carolina State and Georgia Tech on Sunday.
The Tar Heels led 7-1 until Boston College (31-27) scored four times in the sixth. North Carolina responded with three runs in its half of the inning and three more in the eighth.
The surprising Eagles, seeded 12th, used seven pitchers. John Witkowski (1-1) took the loss.
Danny Serretti had two hits and three RBIs for the Tar Heels, and Ike Freeman and Dallas Tessar each drove in a pair of runs. Tessar's bases-loaded single in the sixth doubled his RBI total for the season.
Hansen Butler (3-0), who saved the Tar Heels' victory against Miami on Friday, worked 1 1-3 innings and was awarded the victory.
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