Goggin had a 12-under 204 total. Australians Geoff Ogilvy (67) and Rod Pampling (68) were tied for second. Pampling won the Australian Masters last week.
Ogilvy, the 2006 U.S. Open champion, holed a 50-foot birdie on the 18th hole, his third birdie in his last six holes.
Jarrod Lyle, the Australian who equaled the course record with a 63 on Friday and led for much of Saturday, went the other way. Lyle bogeyed three of his final six for a 71 to drop into a tie with countryman Peter OMalley (67) at 10 under.
Australias Chris Gaunt (68) and New Zealand left-hander Tim Wilkinson (69), the first-round leader, were tied for sixth, three shots back.
Tim Clark of South Africa (69) was nine back at 3 under.
Goggin, the second round co-leader with Lyle, said he had an inconsistent day on the greens.
It was nice to finish the way that I did after a couple of three-putts earlier in the round, Goggin said. I gave some shots away early, so to finish with three birdies on my last four holes was great.
Goggin hit a 6-iron to 2 feet on the 18th, setting up a near tap-in birdie. But hes not getting too excited about a one-shot lead.
It is kind of irrelevant, he said. You are playing with good players, so you just have to go out and shoot the best score of the day. You cant leave anything on the ground.
Ogilvy also had a difficult day with the putter, making the chip on 18 all the more special.
It was a relatively simple chip-and-run that I was trying to get close, Ogilvy said. It was a big bonus to go in. Maybe it was good karma for all the putts I missed today.
Lyle moved two strokes ahead of the field with an 8-foot birdie putt on the par-3 11th, but an errant tee shot on 13 cost him his first bogey of the day, reducing the lead to one.
The 27-year-old Lyle, who survived leukemia as a teenager, birdied the par-5 15th just as Ogilvy birdied 18. But Lyles bogey on 16 when his approach flew past the pin and off the green created a brief four-way tie before Goggins late birdie.
With thunderstorms forecast for later in the day, organizers put the third-round groups off both tees and with earlier start times.
Due to a backlog from a thunderstorm suspension Thursday, six groups had to finish their second rounds Saturday morning, when the cut was made at even-par 144. That meant defending champion Peter Lonard, at 1 over after a 75 Friday, did not qualify for the weekend.
John Daly wasnt around either, having missed the cut by four shots following a second-round 77 and after being plagued by putting problems. But tournament organizers said they would be happy to have him back.
Daly was making his first appearance here since throwing his ball and putter into a pond off the 18th green in 2002. He was also disqualified then for failing to sign for a 78 on his scorecard, but would have missed the cut anyway.
Were disappointed to lose him but I am extremely disappointed more for John because I think tee to green, hes played particularly well on a course that doesnt really suit him, PGA of Australia chief executive Max Garske said. Unfortunately for him the short stick hasnt worked.
Garske said he wouldnt rule out attempting to lure Daly back next year.
If he is prepared to come back we will always have him, Garske said.
Daly only decided a few weeks ago to play here, but the move by organizers to secure him paid dividends ' attendance for the first two days was up nearly 5,000 from last year.
He also missed the cut last week at the Australian Masters at Melbourne. Daly will play next week in the Australian Open at Royal Sydney.