Seven-time world champion Loeb finished tenth, also benefiting from team orders, after Citroen colleague and French compatriot Sebastien Ogier slowed on the penultimate stage.
Loeb, who finished 10th, salvaged four points from the event, three of them for winning the final Power stage, while 11th-placed Ogier finished pointless.
With three rounds in Europe remaining, Loeb leads on 196 points from Hirvonen 181, Ogier 167 and Latvala 116.
It was a third Rally Australia victory for Hirvonen, who also won in 2006 and 2009 on different courses while Australia didn't stage an event in 2010.
His only previous triumph this season was in the opening round in Sweden, with Loeb and Ogier each subsequently notching four victories.
"This is a fantastic feeling and a very important result for the team and for my championship chances," Hirvonen said.
Latvala was philosophical about surrendering his opportunity to win: "Of course, it would have been great to have won the rally but it was a great result for the team."
Both Loeb and Ogier lost valuable time on Friday after each crashed while leading.
"I can't be happy with this rally," Loeb said.
"It has not been good for me, my teammate or my team."
His sentiments were shared by a despondent Ogier, who was more compliant on Sunday than in the previous round in Germany when he won after ignoring team orders to let Loeb take first spot.
"I have team orders and I respect it," Ogier said.
New Zealander Hayden Paddon clinched the Production Car World Rally Championship title by finishing sixth overall in his Subaru Impreza.
"It's been absolutely perfect. A few months ago, we had no money and no campaign but, thanks to the people back home in New Zealand, we've come here and won the title," Paddon said.
"It's awesome and we'll try as hard as we can to come back next year in something bigger and better."
- AAP
