The Rotorua professional had an up and down run after the turn that saw him make three birdies and three bogeys in a six hole stretch where he lost pace with Guthrie.
Lee obliged with a bogey at the par-five 15th to fall back to 16-under par. He would close with three straight pars and come up short in his attempt to become the first player in Tour history to successfully defend a title.
Australian Cameron Percy stumbled with consecutive bogeys at 16 and 17 to fall out of the lead, which belonged to Guthrie after he rolled in a 22-foot birdie putt on 17.
Playing in the third-to-last group, Guthrie then made an exceptional par-save on the 470-yard, dogleg-right finishing hole.
"I probably should have pulled a 3-wood off the tee," he said. "And not hit driver."
His tee shot went through the fairway and settled amongst some trees that guard the left side of the hole. Guthrie had 146 yards to hole and punched an 8-iron under the trees. The ball bounced in, then out of the front, greenside bunker and nestled in the rough. His pitch came up short, setting up his "biggest clutch putt as a professional".
Guthrie's 66 was the low round of the day and he headed to the practice range expecting either Lee or Percy would make a birdie and force a playoff. Neither got close after each wound up in the same trees that Guthrie found 20 minutes earlier and each settled for par.
"I missed my flight home so it looks like I'll miss class again tomorrow," said Guthrie, who is juggling golf with school and finishing up 13 credits for his business degree at the University of Illinois.
"I'm going to meet with the teacher and catch up on my homework but then head to Chicago for the weekend."
Defending champion Lee came one shot shy in his attempt to become the first player in Web.com Tour history to successfully defend a title. He joined three others who came close to repeating their wins.
He climbed from 157 to 73 on the web.com Tour money list after only four events in 2012.
With the FedExCup Playoffs now concluded Lee will return to the PGA Tour Fall Series where he has to improve from 159th to inside the top 125 players to keep his card for 2013.
Manawatu professional Tim Wilkinson carded a three-under par 69 to finish on a 10-under par total seven shots back from Guthrie.
The former PGA Tour pro, who began the week in 59th on the web.com Tour money list, had rounds of 67, 71, 71 and 69 at the Midland Country Club to climb eight spots to 51.
Hamilton professional Steven Alker had a one-under par 71 to finish in a share of 45th place and slip one place to 88th on the Order of Merit.
Meanwhile, on the Japan Golf Tour New Zealand amateur rep Vaughan McCall has finished in a share of 53rd place at the Asia-Pacific Panasonic Open.
The 21-year-old from the Gore Golf Club carded rounds of 70, 70, 75 and 70 for a one over par total to finish in a share of second place on the amateur standings, 10 shots back from Australian Cameron Smith.
McCall will travel to Turkey this week where he is preparing to play in the Eisenhower World Amateur Team's Championship alongside Ben Campbell and Mathew Perry.
Perry also played in the event and shot rounds of 72 and 76 to miss the cut.
Rookie professional Ryan Fox, who was playing for the first time on the Japan Golf Tour, missed the weekend with rounds of 72 and 71.
