His total of 134 established a new tournament record breaking the old mark of 135, set last year by Adam Groom.
Chris Tidland fired a 4-under 68 in the second round to climb into a share of second place. Tidland stands at 5-under-par 139 and was joined there by Dan Olsen (70), Brent Schwarzrock (69), Greg Chalmers (71), Keoke Cotner (70) and Brian Kortan (70).
Bowditch began his second round on the back nine at Royal Adelaide Golf Club. The young Australian picked up a birdie at the 11th to move to 6 under.
The 21-year-old tripped to bogeys at 14 and 16, but carded a birdie in between at the 15th. Bowditch parred his final two holes to head to the front nine at minus-5.
Bowditch dropped in back-to-back birdies from the first. He drained another birdie try at the fourth to move to 8 under.
The Australian kept going with a birdie on the par-4 sixth. Bowditch capped his round with a birdie at the par-5 ninth.
'On the back nine, I really started to hit my driver really well and got myself into some good positions,' said Bowditch. 'I sort of just made the most of them.'
Tidland carded three birdies over his first 10 holes to move to minus-4. However, he stumbled to a bogey at the 11th before picking up consecutive birdies from the 15th to share second place.
Cotner, the 2000 Oregon Classic winner, got off to a rough start with a bogey at the 11th, his second. He erased that mistake with an eagle at 15 and a birdie at 16 to get to 5 under.
The 33-year-old tripped to a bogey at the 17th though. Around the turn, Cotner carded birdies at the second and fourth before tripping to another bogey at five. He parred out to remain at minus-5.
Olsen also began on the back nine and started with a birdie on No. 10. The 38- year-old converted consecutive birdies from the 14th to get to minus-6. He ran off eight straight pars around the turn. He tripped to a bogey at the sixth, then parred his final three holes.
Schwarzrock opened with five straight pars before a double bogey at the sixth dropped him back to even-par. The 32-year-old birdied four of his next five holes to get back into contention. He picked up one more birdie at the 15th to join the crowd in second place.
Chalmers got off to a quick start with birdies at the first and third to get to 6 under. The rest of the round was a roller coaster ride though. The Australian stumbled to back-to-back bogeys from the fifth.
He erased those errors with birdies at nine and 10. Chalmers bogeyed the 11th and double bogeyed 12 to slide back to minus-3. He came back with birdies on 14 and 15, but tripped to another bogey at the 16th. He closed his round with a birdie at the last to get back to 5 under.
Doug LaBelle II and Deane Pappas each posted rounds of four-under 68 Friday to move to 4-under-par 140. They were joined in a share of eighth place by Barry Cheesman, who carded a second-round 70.
Cliff Kresge, who shared the first-round lead with Bowditch, stumbled to a second-round 74. He is one of 14 players tied for 11th place at minus-3.
The cut line fell at 1-over-par 145 with 72 players advancing to the final two rounds. Among those missing the cut was 2004 champion Euan Walters, who struggled to two straight rounds of 5-over 77.