Bernard Foley continued his impressive goal-kicking with 14 points as the Wallabies posted a seventh-straight test win - a feat they last achieved in the 1999-2000 season.
"I was pretty happy with the intent across the game, I don't think we confused anyone with what we were trying to do," said McKenize. "We dominated possession, territory ... we just didn't make the most of every opportunity.
"To get three wins in a row, that is the best possible thing we can do in terms of taking confidence forward."
Guilhem Guirado scored a consolation try for France, who have not won in Australia in their past 11 tests dating back 24 years.
It was the second heavy defeat for the tourists in the series, after a 50-23 mauling in Brisbane in the first test, before an improved defensive performance in the 6-0 win by the Wallabies in the second match in Melbourne.
"Today Australia won all the contact areas," France coach Philippe Saint-Andre said.
"They go forward all the time, they had a big tempo to the game and we missed so many tackles. There was more activity, more urgency, more skill in the Australian team than in our team."
The Wallabies assumed the ascendancy early as they jumped out to a 10-0 lead through a penalty and a converted try to Skelton and then took advantage when prop Rabah Silimani received a yellow card in the 26th minute for tackling winger Adam Ashley Cooper without the ball.
France came under huge pressure and did well to limit the damage to 20-6 at the break.
The second half began as the first ended, with Australia probing the French defensive line and it took only two minutes for Skelton to offload a clever short pass to Folau to send the fullback through untouched to score under the posts for his 13th test try in only 18 matches.
They added further tries to captain Michael Hooper, and replacement halfback Nick Phipps to complete the rout.
Australia 39 (I. Folau 2, W. Skelton, M. Hooper, N. Phipps tries; B. Foley 4 cons, 2 pens), France 13 (G. Guirado try; M. Machenaud con, pen; B. Dulin pen). Halftime: 20-6. AAP