The pair finished 54 holes at 15-under 198 and is three ahead of overnight co-leader Darron Stiles (70), Peter Tomasulo (63) and Kyle Reifers (65) at the TPC at Craig Ranch.
This is the final event of the season on the Nationwide Tour and after the completion of the final round, the top-25 players on the money list will earn PGA Tour cards for next year.
Bettencourt is 12th on the money list and is safe for a trip to the PGA Tour next year. He can win the money title, but Molder is 32nd and in need a strong finish if he is to return to the PGA Tour.
'You go out and try to hit the fairway on the first tee and oversimplify things,' said Molder. 'I'm going to try and win the golf tournament. I feel very comfortable with my game.'
Bettencourt birdied one, but lost that stroke at four. After the hiccup at the fourth, Bettencourt went on a major tear.
When his 11-foot birdie putt at the eighth fell into the cup, that was his fourth in a row. He drained a 22-foot eagle putt at nine to cap off a front-nine 30, but he wasn't done.
Bettencourt played a spectacular approach to 3 feet to set up birdie at the 10th. That birdie meant Bettencourt played hole Nos. 5-10 in 7 under par.
Bettencourt parred 11 and 12, but his approach spun back inches from the hole at 13. He tapped in for birdie and made it two in a row with a 9-footer at the 14th.
That put Bettencourt in front by four, but Molder flew up the leaderboard. Molder birdied four in a row from 12, including a 12-footer at the 15th and was only two behind.
Bettencourt, after a great 12-foot par save at 16, missed the green at the par-three 17th and walked off with a bogey. That cut his margin to one and that disappeared when Molder birdied the last.
'This is so much fun,' said Bettencourt. 'Big day tomorrow, fun day regardless of the outcome. It'd be great to finish first, but there's a lot more on the line.'
Garrett Osborn, who shared the second-round lead with Stiles, only managed an even-par 71 and is tied for sixth place with Marc Leishman, who posted a 68, at minus-11.