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Hosts Australia have made the quarter-finals for the last 15 home events but needed to beat South Africa by five points to guarantee qualification for the knockout stages.
Australia went into overtime leading 24-21 and conceded a penalty with South Africa looking to win themselves. But Australia forced a turnover and they broke three-on-one, with Malouf powering to the try line 90 seconds past the hooter.
They had led 17-0 through Jeral Skelton and Lewis Holland’s double but South Africa produced a sucker punch either side of the break, with Justin Geduld’s pair of tries and Stedman Gans putting the Blitz Bokke ahead.
Geduld was carded for a deliberate knock on and Australia capitalised through Josh Coward before the overtime dramatics.
It means Australia can still retain their Sydney title, but finishing second has handed them a tricky draw against Fiji, the winners in Cape Town and Hamilton.
The winner of that tie will play either New Zealand or France. The other quarter-finals see South Africa play England and USA take on Spain.
Ireland's impressive run continued at the HSBC Sydney Sevens 2019 on Saturday as they reached their first-ever HSBC World Rugby Women's Sevens Series Cup semi-final following a 22-7 defeat of Spain at Spotless Stadium.
The Irish, who topped a pool for the first time on day one, will now face defending champions Australia in the semi-finals on Sunday after the hosts maintained their perfect record over France on the series with a 21-17 win.
The other Cup semi-final pits series leaders New Zealand, who are bidding for a sixth series title in a row, against Glendale runners-up USA.
New Zealand ran out 17-7 winners over Canada in a scrappy opening quarter-final, before Cheta Emba's last-gasp try saw USA beat Russia 7-5, co-captain Nicole Heavirland's conversion proving the difference in the tight affair.
The top eight teams now take a break until Sunday with the fifth place semi-final between Canada and Russia kicking off proceedings at 08:50 local time (GMT+11), with the first Cup semi-final between the Black Ferns Sevens and USA set for 09:34.