Michael Russell and Mike Zolk both had two RBI in the eighth to break the game open and knock the Wolfpack out of the NCAA Tournament.
North Carolina will again try to avoid elimination on Friday when it meets unbeaten UCLA.
A win by the Trojans in that one will put them into the best-of-three championship series against either Mississippi State or Oregon State. If North Carolina defeats UCLA, those two teams will face each other again Saturday to determine which one will advance.
Mississippi State and Oregon State will also play on Friday -- the Bulldogs needing only one more win to get to the championship round.
Johnson went 8 1/3 innings for North Carolina against its old Atlantic Coast Conference rival, walking two and striking out six. The Tar Heels avenged a loss to the Wolfpack in the opening round of the College World Series.
North Carolina opened the scoring in the fourth on a bases-loaded sacrifice fly from Russell and Colin Moran singled in a run in the fifth for a 2-0 lead.
The Tar Heels took control in the eighth when Russell drove in two runs with a single and Zolk delivered a two-run double.
Carlos Rodon gave up the first two North Carolina runs to take the loss.