It was Maggert's first win since 1999 at the WGC-Accenture Match Play Championship.
He was 9-under 271 for 72 holes while Pernice (71) was 6-under 274. John Cook (71) and Kris Cox (72) tied for third place at 4-under 276.
"It's been a strange career, but I've had a great time playing golf out here," said Maggert, who won $936,000. "I would have bet that I would have won more times by now. But with five kids at home, I have a lot of other priorities that are important to me in my life. I'm very fortunate that I can still come out here at the age of 42 and still win."
Third-round co-leader Tom Herron (77) tied for 16th place at even-par 280.