The Pacers (41-11) had dropped its opener, 7-4 to Montevallo, on Wednesday.
USC Aiken will have to wait and see if it earns an at-large bid to the Division II Baseball Championship. The Pacers are currently ranked second in the Southeast Region.
Six teams from the region will receive invitations to the tournament.
The selection show is scheduled for 10 p.m. Sunday.
Bryce Baur hit a home run off the scoreboard in the top of the first inning to give the Pacers a 1-0 lead against UNC Pembroke, but it didn’t last long as UNC Pembroke scored the next nine runs.
Branden Millhouse was the only Pacer with multiple hits, going 2 for 3.
Zade Denton led UNC Pembroke (37-15) with four hits.
USC Aiken starter Wyatt Brown (6-4) took the loss.