Nathan Green carded a 4-under 67 in chilly conditions to take second place at 12-under-par 201. Keith Huber is one stroke further back at minus-11.
Danny Ellis, Brian Henninger and Troy Matteson, a two-time winner this season, share fourth place at 10-under-par 203.
Chalmers got on the board with a birdie at the par-5 third. He dropped a shot at the par-4 sixth to slide back to minus-11.
The Australian made the turn at 12 under as he dropped in a birdie putt on the ninth. Around the turn, Chalmers bogeyed the 11th to again drop to 11 under.
Chalmers parred four straight holes. His par on 15 wasn't pretty. He hit a tree with his tee shot and was forced to pitch sideways with his second. Chalmers' third shot to the 293-yard hole came from 205 yards out. He stuck that within 5 feet and made the putt to save par.
'I've only got to hit it about 200 yards there to have 95 or 100 yards to the green,' Chalmers said of the 15th. 'I've tried to lay it up there three days in a row. It's the toughest shot for me because I don't cut the ball.'
Chalmers then rolled in an eagle putt from 40 feet out to jump to 13 under. The 31-year-old parred his final two holes at Hillcrest Country Club.
'Through that stretch of holes, I could have made three bogeys and I wind up making three pars and an eagle,' said Chalmers of holes 13 through 16. 'I saved myself a bunch of shots there. It was kind of exciting. Up to that point, I hadn't hit terrible shots, I just hadn't hit any great shots.'
Green played the front nine in even-par. He birdied No. 2, but stumbled to a bogey at the next while parring the other seven holes on the front nine.
The 30-year-old got to 9 under with a birdie on the par-4 12th. Green made it two straight as he birdied the par-3 13th. After a par at 14, the Australian ran in another birdie try on the par-4 15th.
Green then birdied the 16th to get to minus-12. He parred his final two holes to remain one shot behind Chalmers.
Jason Schultz is alone in seventh place at 9-under-par 204 after a 2-under 69. Cliff Kresge fired a 5-under 66. He moved into a tie for eighth at minus-8 and stands alongside Camilo Villegas and Charley Hoffman.