Fiji were the only other unbeaten team in Pool B with the Australians but with 11 team changes they were more focused on their winner-take-all game against Wales in Nantes on September 29.
The Wallabies join South Africa in the quarter-finals and will play either England or Tonga, who face off on September 28 in Paris.
Matt Giteau, playing in his 50th Test, was named man-of-the-match with 27 points from two tries, four conversions and three penalties, while winger Drew Mitchell scored a hat-trick of tries.
The Wallabies looked lethargic for most of the opening half but still went to the break leading 22-5 after three tries, two of them to inside centre Giteau.
The Fijians looked lively in passages, but it was Giteau who opened the scoring in the 17th minute after good lead-up work from Wycliff Palu and Lote Tuqiri.
Flyhalf Berrick Barnes, in the side for the injured Stephen Larkham, delivered some beautiful passes but the Australians lacked penetration out wide, clearly missing the thrust of Stirling Mortlock, injured skipper and outside centre.
The Wallabies struggled to clear the ball from lineout wins and mauls, but increased their advantage in the 31st minute when a Chris Latham grubber enabled Mitchell to dive on the crumbs and score for 17-0.
Vereniki Sauturaga, Fijian hooker, was penalised twice for taking too long for throwing into the lineout before Giteau claimed his second try four minutes from the interval when spinning out of a tackle to plunge over, pushing the lead out to 22-0.
Fiji fightback short-lived
Fiji hit back right on halftime when winger Isoa Neivua carried three tacklers over the line to score in the left-hand corner for his team's first try.
A Giteau penalty and a Barnes drop goal increase the lead to 28-5 in the minutes after the resumption, before Fiji skipper Mosese Rauluni came on after halftime and surged through an embarrassing hole in the Australian lineout to send open-side flanker Aca Ratuva racing over unopposed with Seremaia Bai converting from wide out for 28-12 after 46 minutes.
Giteau steadied with a 50th-minute penalty to boos from the 32,231 crowd looking for the Wallabies to attack more rather be conservative, and the Australians took heed when quick hands from Giteau put centre partner Adam Ashley-Cooper over for the bonus-point fourth try on 57 minutes and a 38-12 lead.
With the match all but won, John Connolly, Wallabies coach, cleared his replacement bench for the last 20 minutes. The margin blew out in the final 10 minutes with Mitchell scoring two more tries and replacement forward Stephen Hoiles also crossing.
Murrayfield mauling
Meanwhile, in the late game Scotland's second-choice side was handed the anticipated thrashing by 40-0 as New Zealand booked another berth in the Rugby World Cup quarterfinals.
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Doug Howlett scores against Scotland
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Scotland's key players were rested for the winner-takes-all match with Italy next weekend and their backups, including two new caps, gave a gritty effort but were clearly outclassed.
The All Blacks scored six tries, two by winger Doug Howlett to claim the New Zealand test tryscoring for himself, and the Scots were kept scoreless for the first time since March 2004, when France won 31-0 at Murrayfield.
Captain Richie McCaw, Byron Kelleher, Ali Williams and Dan Carter scored
the other tries, and Carter landed only four of eight attempts.