Noah Lolesio kicked a last-minute penalty as Australia recovered from an early red card to beat France 33-30 and claim the three-Test series 2-1.
Baptiste Couilloud and Cameron Woki scored tries for the visitors as Tate McDermott and Lolesio crossed for the hosts with the game tied at the break.
The sides exchanged second-half tries before Lolesio struck the winning kick.
Australia lost winger Marika Koroibete in the fifth minute for a high tackle on France captain Anthony Jelonch.
The Wallabies' ninth consecutive win at Suncorp Stadium in Brisbane ensured they won a tight series, in which the previous two games had both been decided by two points.
Australia squeezed home in the first Test thanks to a French error, before France claimed their first away win over Australia since 1990 in the second Test to ensure the series went to a decider.
Elsewhere, New Zealand cruised past Fiji 60-13 to claim their series 2-0.
Fiji-born winger Sevu Reece scored three first-half tries against his native country, before the All Blacks added another six after the interval.