Michalak, who had not played on home soil in the French shirt since a Six Nations game against Ireland in 2010, was replaced in the closing stages to a standing ovation after kicking 15 points and brilliantly setting up Wesley Fofana for France's second of three tries.
Philippe Saint-Andre's side relied on an utterly dominant scrum but also the raw power of Louis Picamoles, who scored first, to prevail against Australia with also a penalty try and a Morgan Parra penalty.
The visitors had their chances late in the first half but poor execution meant that they left the pitch with only two Mike Harris penalties to show for themselves.
"We had a revenge to take against Australia," Michalak said, referring to a 59-16 defeat France suffered at the hands of the Wallabies two years ago.
"Against such a team, we had to play at a high level. but we must look forward, because it is going to be as hard against Argentina.”
Nathan Sharpe added: "France played very well and thoroughly deserved to win.”
France's biggest win over Australia since a 34-6 victory at the Parc des Princes in 1976 was a huge boost as they look to improve from their fifth place in the IRB rankings ahead of the 2015 World Cup seedings.
Australia continued with Kurtley Beale at fly-half after the 23-year-old impressed in a 18-18 draw against New Zealand in October.
France relied on the experienced Michalak to steer the ship with Maxime Machenaud starting at scrum-half for his second cap.
Australia had thrashed France on their last visit to the Stade de France two years ago but were on the other end of the game this time.
France put on the early pressure and were rewarded after five minutes when Michalak whipped a penalty kick between the posts after a Wycliff Palu offside.
Harris quickly responded with a penalty but Les Bleus were soon back in the Australian half.
Australia conceded a penalty for turning the scrum five metres from the line and France opted for another scrum from number eight Picamoles charged over the try line.
Harris slotted another penalty after Australia had threatened the French line through Adam Ashley-Cooper and Tatafu Polota Nau to keep the visitors afloat.
Australia finally got into their stride shortly before the half hour, but poor execution kept them from the France line, with Beale missing a try-making pass near the left wing.
Picamoles gave the hosts their best attacking opportunities as the number eight's forays down the middle proved tricky to handle.
Another devastating Picamoles run led to Michalak's well-executed drop as France opened a 10-point gap on the stroke of half-time.
Australia's scrum creaked as they hardly contained France's brute power and the visitors conceded another penalty early in the second half, only for Florian Fritz's feeble attempt to land far from the posts.
France surged clear before the hour when a poor Beale kick landed in the hands of Michalak, who danced through the field before offloading to Fofana for the centre's fifth try form eight appearances.
The crowd immediately chanted Michalak's name and they soon had more to celebrate.
The Australia scrum once again cracked and referee Nigel Owens gave the hosts a penalty try before Parra rounded it up with a late penalty.
France face Argentina in Lille next Saturday and Samoa a week later at the Stade de France.
Australia play England at Twickenham on Saturday before games against Italy on November 24 and Wales on December 1.