Niclas Fasth, Joakim Haeggman, Alastair Forsyth, Chris Hanell and Simon Nash share second place at 7-under-par 65.
Bowditch vaulted out of the gate at Gulf Harbour Country Club with back-to-back birdies from the first. He added a birdie at the par-4 fourth and birdied two in a row starting at the par-5 sixth to reach 5 under.
The 21-year-old kicked off the back nine with a birdie at the 10th and kept on rolling with a birdie at the par-5 11th. Bowditch then birdied the par-4 12th and picked up a birdie at the par-3 13th to make it four straight.
'If you play well in Australia it's definitely a fantastic chance to get stuck right into the European Tour,' said Bowditch. 'It's a great stepping stone.'
Bowditch struggled on the green at the par-4 14th and three-putted for his first bogey of the day. He countered with a birdie at the par-5 17th but found trouble on the closing hole and dropped another shot after an errant drive.
'Today I hit the ball good and the putts went in as the score showed,' said the Australian. 'I played well last week at the Heineken but couldn't make a putt.'
Fasth played the back side first and birdied three in a row starting at the 11th. He tallied a birdie at the 17th to make the turn at 4 under and collected another birdie at the par-3 third.
The Swede then birdied three straight from the fifth but a bogey at the eighth left him one shot off the lead.
'It was good out there,' said Fasth. 'The greens were rolling truly but they can't make them much quicker or the slopes will take over.'
Haeggman stood at 8 under with one hole remaining on Thursday but he bogeyed the par-4 18th for his share of second.
Simon Khan, Pierre Fulke, Jarrod Moseley, Adam Crawford, Garry Houston, Martin Maritz, Oliver Wilson and Alistair Presnell share seventh place at 6-under-par 66.
Craig Parry, who won the Heineken Classic last week in a playoff, finished in a group at 4-under-par 68.