'I have been playing well and I think the biggest difference is my putting,' said Pappas, a 33-year-old native of South Africa who won the Greater Cleveland Open last year. 'I'm making the putts that I'm supposed to make.'
Cotner fired an 8-under 64 on Sunday to vault toward the top of the leaderboard, while Petrovic also made a big move on Sunday with a 5-under 67.
Chris Couch, who shared the lead with Pappas after Saturday's third round, managed only a 1-under 71 on Sunday and finished tied for fourth with John Kernohan, Tommy Biershenk and Pappas' brother, Brenden.
Couch got off to a hot start with birdies on three of his first four holes, opening a two-shot lead over Deane Pappas. Pappas, who birdied the first hole, added a birdie at No. 7 while Couch made a bogey for a two-shot swing that left the two tied again at 16-under-par.
Pappas followed with another birdie on the par-4 8th to take the lead, which he carried to the back nine.
'I felt the momentum did swing in my favor as far as the two of us were concerned, but anything can happen on that back nine and I knew that there were a bunch of players that were pretty close,' said Pappas.
Pappas extended his lead to three shots when he birdied the 10th hole and Couch dropped another shot with a bogey. Couch wasn't a factor the rest of the way, managing only pars on the final eight holes.
Pappas, meanwhile, was 18-under-par and his closest pursuer, Cotner, was already in the clubhouse at minus 16. Pappas parred the 11th, but sandwiched a birdie around two bogeys over the next three holes to leave his lead at just one shot.
'I was keeping a close eye on that leaderboard,' Pappas said. 'I knew at the par-3 16th that the two 16-unders (Cotner and Petrovic) were in the clubhouse. Then it went back to me and Chris.'
Couch was still two off the pace as the two went to the 17th and Pappas drained a 25-footer for birdie to extend his lead to two over Cotner and Petrovic and three over Couch.
Pappas needed the extra cushion. He found his ball under a tree at the 18th hole and had run a shot into the bunker that guards the green. He then blasted out and missed a five-footer for par, but tapped in for bogey and the win, earning a first-prize of $81,000.
Cotner made four birdies on the front and back nines for his final round of 64. He birdied the 17th and 18th to make a run at the top, but ran out of holes.
Petrovic's round was highlighted by four birdies after a bogey at the 10th.
Couch, who won last week's season-opening Florida Classic, was looking to become the first back-to-back winner on the Buy.Com Tour since 1997.
'I got off to a great start with birdies on one, three and four,' said Couch. 'I hit 15 greens...I just couldn't get a putt to fall. I missed a lot of good putts that went right over the edge. I guess it just wasn't my day.'
Click here for full-field scores from the Buy.Com Monterrey Open