Australians Stuart Appleby and Nick O'Hern finished tied for second with 41 points.
Casey led by six points to start the final round at New South Wales Golf Club and jumped out of the gate with birdies on each of the first two holes. However, Casey struggled with a bogey at the very next hole and dropped another shot at the par-3 sixth.
The Englishman recovered with a birdie at the seventh to make the turn with 43 points. Casey added to his advantage with a birdie at the 10th to reach 45 points but the wind that persisted for most of the day eventually caught up with the 25-year-old down the stretch.
Casey had two straight bogeys starting at the 15th and was in danger of making it three in a row after he missed the green at the par-3 17th. Casey found a bunker off the tee and blasted his second shot 20 feet from the cup. He remained calm and drained the putt to save par and keep his challengers at bay.
'The first time I looked at the scoreboard all day was 17,' said Casey. 'I knew what Stuart was but I had no idea what anybody else was. The calculations started to go through the head very quickly and I figured I needed to make that.'
At the closing par-5, Casey picked up his fifth birdie of the round to secure his second career title on the European Tour.
'The first one was tough,' said Casey of his victory at the 2001 Scottish PGA Championship. 'I have no idea if the second is tougher. They're all tough. It shows the first wasn't a flash in the pan so that'll probably answer a few critics out there.'
Appleby, who played alongside Casey in the final group, was in contention late and just missed an eagle at the 18th after his chip shot failed to find the bottom of the cup. The 31-year-old finished with five birdies and two bogeys for eight points.
Peter Lonard was on fire early with an eagle at the par-four first and added four birdies on the front side. Lonard continued his fine play on the inward half with a birdie at the 10th and back-to-back birdies from the 12th to raise his total to 42 points.
The Australian's attempt at a comeback fell apart at the very next hole, however. Lonard faltered with a double-bogey at the par-4 14th to finish tied for fourth with 39 points along with Jarrod Moseley.
Greg Turner had 18 final-round points to finish alone in sixth with 38. He was followed by Martin Doyle and Scott Hend, who tied for seventh with 37 points.
Peter Senior and Robert Karlsson tied for ninth with 35 points.
The tournament was played using the modified stableford scoring system which promotes aggressive play. The scoring awards eight points for a double-eagle, five points for an eagle, two for a birdie and none for a par. One point is deducted for a bogey and three points are taken away for a double-bogey or worse.
This event was co-sanctioned by the European and Australasian Tours.