Fly-half Camille Lopez kicked 16 points while Sebastien Tillous-Borde and Teddy Thomas scored first-half tries as the hosts lead from the outset.
Australia had Bernard Foley to thank for keeping them in contention, as well as tries in either half from Adam Ashley-Cooper and Rob Simmons.
Remi Tales was sin-binned with six minutes remaining but France hung on.
Both teams were coming off the back of wins last weekend. France eased past Fiji 40-15, while Australia beat Wales 33-28 in Cardiff.
Scrum-half Tillous-Borde gave France the ideal start with a try seven minutes in after he picked up the ball from the base of a ruck five yards out.
Winger Thomas then thrilled the home crowd with a stunning run through five tackles to score in the corner and stretch France's advantage to 17-6.
Ashley-Cooper replied for Australia seven minutes later after smart work from Foley enabled him to collect a switch pass just inside the touchline.
France kept the Wallabies quiet for the majority of the second half until Tales' infringement made for an uncomfortable finish.
Second row Simmons exploited the gaps to cross over after a smart offload from replacement Quade Cooper.
Foley converted to put them within three points, but Australia missed the chance to grab a late win as James Horwill knocked-on 10 metres out.
France made it two wins from two autumn internationals as they withstood a late surge from Australia in Paris.