Ryuji Imada finished second, Phil Tataurangi took third at 11-under-par and Todd Fischer came in fourth at minus-10.
Maginnes held a three-shot lead overnight but a bogey at the second hole coupled with a birdie by Tataurangi at the first dropped the lead to one.
Maginnes comments on his Carolina Classic win
Tataurangi birdied the fifth to tie Maginnes at the top of the leaderboard and then birdied the next to get a one-shot lead. The lead did not last long as Tataurangi went double-bogey, bogey, double-bogey from Nos. 9 through 11 to drop out of contention.
Maginnes birdied No. 11 when he drained a 30-foot putt to get a two-shot margin, but he dropped another stroke at No. 12 when he missed a three-foot par save. He reclaimed the lost stroke with a two-putt birdie at the par-5 13th and followed with a 15-foot birdie at No. 14 to extend his lead to three.
Maginnes holed a six-foot par save at No. 15 after Imada ran home a 15-foot birdie at the same hole. Maginnes cemented the win when he drilled a two-footer at the last to save par.
'The year has really just gotten started and this puts me in good position for everything,' said Maginnes, who earned $81,000 for the victory. 'I don't know what it does for me on the money list but I won't even look at that until September anyway.'
He jumped to eighth on the money list with his third victory on the Buy.Com Tour. Maginnes previously won the 1995 San Jose Open and the 1998 Dakota Dunes Open.
Imada carded a 69 on Sunday, but it was not enough to catch Maginnes.
'I knew today was going to be a hard day with the way the wind was blowing in different directions,' Imada said. 'My goal was to hit all the fairways and greens, which I did pretty well except a few holes, but I couldn't capitalize on a few of the easier holes that I should have made birdies. John made some good birdies coming in and also good up and downs and that was the two-shot difference.'
David Kirkpatrick, Paul Claxton, Willie Wood and Tim O'Neal shared sixth at 7-under 277.
Full-field scores from the Buy.Com Carolina Classic