Perez had two hits and three RBI including his fourth homer of the year for the Lookouts, who lead the current six-game series 2 wins to 1.
Carolina scratched out a run in the second before Perez' two-run shot in the bottom of the frame gave the hosts a 2-1 lead.
The Mudcats didn't get a hit off starter Alberto Bastardo until the sixth, when Michael Griffin (pictured) stroked a leadoff double to left. Zack Cozart's sac fly later tied the score at 2-2, but Chattanooga scored twice in the bottom of the frame including Perez' RBI single to end the scoring.
Tom Cochran (1-1) worked 5 1/3 innings in the loss, allowing five hits and four earned runs. Kendy Batista (4-0) got the win in relief.
Carolina had two transactions on Tuesday, when left-hander Steve Otterness was returned to Dayton while Chris Kelly came off the disabled list.
Carolina's Lee Tabor (0-0, 3.68) will make a spot start against fellow lefty James Adkins (2-6, 5.19) in today's 11:15 a.m. affair.