Having already secured the title by beating Spain 35-0 in the quarter-final of the fifth leg, Australia were beaten 29-19 by Canada, their second loss of the season, in Clermont-Ferrand.
The win comes less than three months before the competition's first appearance at the Olympics in Rio.
"To come out on top in the World Series is an extraordinary effort and we have so much to be proud of this season," coach Tim Walsh said.
"Defence wins championships and up to that last game we had been fantastic all year."
That defence fell by the wayside in the final of the French leg as Canada gained 26 points in the first half, with Australia trailing by 19 going into the break.
A push in the second half saw that gap narrowed, but a late penalty to the Canadians ensured their ten point win.
"It's a bit bittersweet I guess, as we just didn't perform in that Cup Final and Canada ran out worthy winners," Walsh said.
"If you don't make tackles you don't win games and it certainly wasn't our greatest defensive effort.”
"It wasn't a case of us not being up for it - every time we pull on the jersey we are up for it - but it wasn't our game this time around."
Australia finished on 94 points, 14 ahead of previous Champions New Zealand, while Canada and England tied for third on 74 points.