Pernice shot 1-over-par 73 in the final round, but managed to collect one point using the modified Stableford scoring system.
Pernice comments on his second PGA Tour win
That point proved to be the difference between first and second place, as Pernice finished the tournament at +34, one point more than Chris Riley (72, +4).
'The good Lord willing, I held on,' said a relieved Pernice, who collected $720,000.
Defending champion Ernie Els (71, +6), Chris DiMarco (73, +4) and Vijay Singh (72, +2) tied for third place at +32.
DiMarco appeared ready to run away with the tournament early Sunday. He birdied the 5th, 6th and 7th holes at Castle Pine Golf Club, and then rolled in a putt from off the green for an eagle-3 at the par-5 8th.
With birdies worth two points each and an eagle worth five, DiMarco quickly picked up 11 points in four holes to take a six-point lead at +39.
Then everything went horribly wrong.
DiMarco proceeded to his three balls into the water starting at the 9th. He bogeyed the 9th, doubled the par-4 10th, bogeyed the par-4 12th, bogeyed the par-4 15th and made his second double of the day at the par-3 16th.
DiMarco birdied the par-5 17th to enter the clubhouse at +32, which amazingly kept him in the hunt.
That's because DiMarco wasnt the only player who failed to remember that even though the highest score wins, you dont obtain that score by playing poorly.
Pernice, who entered the final round with a three-point lead, also found the water at the 10th and made a double to drop to +32.
He regrouped with a birdie at the 12th and reclaimed sole possession of the lead with another birdie at the 14th.
Leading by three points with three holes to play, Pernice bogeyed both the 15th and 16th holes to drop two points.
Pernices playing partner and good friend Singh couldnt make a move on Sunday. Following a birdie at the 8th to move to +33, the 98 winner of this event parred his next eight holes.
A ninth straight par would have been nice, but instead, Singh bogeyed the par-5 17th to fall to +32, where he finished the tournament.
With no one mounting a late charge, Pernice had the luxury of parring his final two holes to win his first title since the 1999 Buick Open.
'I do my best when I'm relaxed and I enjoy playing with him,' Pernice said of Singh. 'He's one of my best friends out here. We play a lot of practice rounds on Tuesday, so it was definitely to my benefit to play with him.'
Full-field scores from The International