Chalmers completed 36 holes at 9-under-par 133 and is one stroke clear of Matthew Every, who also shot 65 in the second round. His 65 included two eagles on the back nine, as well as an ace at the par-314th.
First-round leader Tom Johnson managed a 1-under 70 and dropped into third place at 7-under-par 135. Jarrod Lyle is alone in fourth at minus-5after a 2-under 69 on Friday.
Chalmers played the back nine first on Friday and he collected his first birdie on the par-411th. After three pars, he stumbled to a bogey on the 15th at Tres Marias Golf Club.
The Australian came right back with a birdie at the par-5 16th. Chalmers followed with birdies on 17 and 18 to make the turn at minus-six.
Chalmers birdied two and five to gain a share of the lead at 8 under.
After briefly taking the lead with a birdie on seven, Chalmers gave that stroke right back as he bogeyed the eighth. However, he closed with a birdie on the ninth to finish one ahead of Every.
'This is a tricky golf course. The hardest thing to do out here is hit the ball the right distance,' Chalmers stated. 'You have elevation of 6,500 feet, a lot of forced carries, up-and-down hills and hitting into a 20-25 mile-per- hour wind. You have to pick the right club at the right time and hope you've guessed right with the wind.'
Every dropped in back-to-back birdies from the first to open his round. He faltered to a bogey at the fourth, but recovered that lost stroke as he birdied the par-5 fifth.
The 2005 U.S. Walker Cupper birdied the seventh before running off five straight pars.
Every tripped to the second bogey of his round on the par-3 13th. He followed with a hole-in-one that jumped him to six-under. Every then eagled the par-5 16th to move to minus-eight.
'I was running a little hot after making bogey at the previous hole,' said Every of his ace, which was the second of three aces on the day. 'The day before I guessed wrong, probably because of the huge elevation drop. Today I just hammered at 9-iron right at it.'
Steve Pate (69) and Jason Caron (70) share fifth place at 4-under-par 138. Jose de Jesus Rodriguez and Michael Putnam are one shot back at minus-three.
The cut line fell at 4-over-par 146 with 62 players moving on to the weekend. Spike McRoy, who had the first ace of the day, made the cut on the number.