Australia led 7-0 in the 12th minute when the players left the field at Ballymore, but lost 21-12.
It was just the second win in nine Tests against Australia for Wales, who are ranked 10th, four places below the Wallaroos.
Wales finished last in the most recent Six Nations women's tournament, losing all five of their matches, but displayed plenty of enterprise on Saturday.
All three of their tries in Brisbane were scored by the backs while both of Australia's five-pointers came from close range forward carries.
The Wallaroos were strong in the scrum, but their lineout struggled as they continued their preparations for next month's World Cup in England.
They had plenty of possession and territory in the second half, but poor passing and handling combined with stout Welsh defence kept them scoreless over the last 40 minutes.
"We had too many dropped balls and we didn't play like we know we can, so I think it's back to the drawing board for us," Wallaroos captain and flanker Emily Chancellor told Stan.
"I think we came out really well in those first 10 minutes after the lightning so you can't really use that as an excuse."Â
It was a fourth loss in six matches this year for Australia, while Wales ended a spell of 818 days without an away victory.
"Bloody awesome, I am genuinely so proud of the girls," Wales captain and No.8 Alex Callender told Stan.
"We wanted to be physical and I think our defence was outstanding today, I'm so proud of the girls."
The Wallaroos had already had a try rubbed out for obstruction before scoring the opening points in the ninth minute, when lock Annabelle Codey plunged over from close range and her try was converted by winger Desiree Miller.
Rain continued to fall after play resumed, but Wales scored from a well executed move from a 21st minute scrum close to the Wallaroos line.
Halfback Keira Bevan and five-eighth Lleucu George combined to send fullback Nel Metcalfe, over, with Bevan converting to level the score.
In an exciting finish to the half, each side scored inside the last two minutes.
George and inside centre Courtney Keight set up Metcalf for her second try with Bevan adding the extras.
A minute later, with just seconds left, Wallaroos No.8 Tabua Tuinakauvadara, smashed over the line from a powerful forward drive off a rolling maul, but Miller couldn't convert.
Ahead 14-12 at the break, Wales added the only points of the second half, with the Influential George's grubber kick setting up a 43rd minute try to centre Hannah Dallavalle, with Bevan again converting.
The teams will play again at North Sydney Oval next Friday.
9°C