Fiji took a 16-12 lead over Australia in the second half at Brisbane's Suncorp Stadium, putting a remarkable World Cup upset within reach.
But James Tedesco helped turn the match around, setting up tries for Kotoni Staggs and Tom Trbojevic, then assisting Trbojevic's second with a grubber. Trbojevic completed a hat-trick as Australia won 36-22.
Fiji five-eighth Kurt Donoghoe created all three tries for winger Semi Valemei, while Brandon Wakeham also contributed to the Bati's strong display. Fiji had never beaten Australia in seven previous Tests; their closest loss was 34-2 in the 2013 World Cup.
Australia secured top spot and a semi-final place in front of 41,108 spectators. The Kangaroos will play at Sydney's Allianz Stadium on Sunday, November 8.
Fiji must beat New Zealand on the Gold Coast on Saturday to reach the knockout rounds. Captain Api Koroisau said, "Even before the game we had a lot of belief and we showed that the way we played," and added, "That belief's only grown going into this game against New Zealand."
Australia coach Kevin Walters said, "I think we need more from everyone. We know we can play better," and praised Fiji's response during the match.