Les Bleus, whose November campaign produced mixed results, alternated moments of attacking flair and periods of costly indiscipline, repeatedly allowing Australia back into a match that fluctuated throughout.
The visitors, who will host the 2027 World Cup with the draw set for December 3, stayed in the fight but faded in the final 20 minutes.
France’s brilliance in broken play yielded tries for Nicolas Depoortere (2), Louis Bielle-Biarrey (2), Julien Marchand and Maxime Lamothe, with Thomas Ramos adding five conversions and a penalty to his own try.
Australia, who also lost to England, Italy and Ireland, capitalised whenever French discipline slipped, hitting back through Matthew Faessler (2), Angus Bell, Max Jorgensen and Josh Nasser, while Tane Edmed kept the scoreboard moving with four conversions.
"We're happy to finish with a big win today," said France captain Gregory Alldritt.
"In defence we need to work a bit, be a bit cleaner as well, less penalties against us. A few steps to work on."
Schmidt, who is stepping down after taking charge following the 2023 World Cup fiasco, praised his team's efforts.
"We’re disappointed we didn’t finish with the victory you would have loved to see," he said.
"But the players have made a heck of an effort - 15 tests in 22 weeks with the amount of travel we’ve had. I admire the way they’ve dusted themselves off and gone again."
The Wallabies scored on the first possession of the game, working through the phases before Faessler bundled over.
France hit back when Bielle-Biarrey ghosted past two defenders and found Depoortere on the inside for the hosts’ first try.
France missed routine tackles to allow Bell to touch down between the sticks and put Australia ahead again before the hosts shifted the ball sharply through the hands to create an overlap, freeing Ramos to glide over and level at 12-12.
France extend lead in style
France extended the lead in style as the ball was worked wide to Bielle-Biarrey and the winger exploded into space, chipping ahead and regathering before stepping inside the last defender to finish a brilliant solo try.
Australia levelled before the break after Maxime Lucu was sin-binned, Faessler crossing again from a maul.
A Ramos penalty and Depoortere’s second try after a quickly-taken penalty gave Les Bleus a 10-point margin but it was not enough for a team who had little focus in defence.
Jorgensen showed impressive pace down the left, kicking the ball ahead before winning the race to dive over in the corner and Edmed converted to narrow the gap to a single point.
The momentum swung yet again when Marchand touched down from a maul and Australia's Tom Hooper picked up a yellow card.
France tightened their grip when a short lineout move sent replacement Kalvin Gourgues slicing through the defence before releasing Bielle-Biarrey who finished in the corner to stretch the lead.
Nasser forced his way over again to bring Australia back to 41-33, but France had the last word with Lamothe’s late try.
The French lost 32-17 to world champions South Africa and beat Fiji 34-21 in their other Autumn internationals.