Referee Andrés Cunha initially waved away Les Bleus' penalty appeals when Antoine Griezmann went down in the box under Josh Risdon's 55th-minute challenge.
But after having another look at the incident on his pitch-side monitor, the Uruguayan opted to point to the spot, with Griezmann converting to put France ahead.
Moments later, Australia were given a penalty of their own - this time without the need for VAR - and Mile Jedinak beat goalkeeper Hugo Lloris from 12 yards to bring the Socceroos level.
A high-tec refereeing tool was also used when France then grabbed a winner with ten minutes left, as Paul Pogba's effort hit the underside of the crossbar and, via goal-line technology, was correctly deemed to have gone in