Les Bleus forward Antoine Griezmann went down in the 18-yard box after a tackle from Josh Risdon in the 54th minute.
Risdon appeared to clip the ball and, as such, the referee didn't give an initial penalty, deeming Griezmann to have gone down too easily.
But once play stopped, the referee checked replays using VAR and perceived that Griezmann had been fouled, despite there appearing to be minimal - if any - contact on the Atletico Madrid star.
Griezmann, who top scored at Euro 2016, coolly and calmly struck the spot kick into the right-hand corner of Australia's net in the 58th minute to give Didier Deschamps' men the lead.
Socceroos supporters in the Kazan Arena booed the decision, which will prove to be a hugely contentious first use of VAR at Russia 2018 and in World Cup history.
Referees are supposed to be 100 per cent sure that a decision is correct if they change after using VAR.
Moments later, however, a handball from Samuel Umtiti on a cross into France's area conceded a penalty in Australia's favour.
Mile Jedinak sent France goalkeeper and captain Huge Lloris in the wrong direction to level the scoring at 1-1 in the 62nd minute - and perhaps do some justice on the Uruguayan referee's decision at the other end that led to them conceding.
Australian soccer fans are familiar with VAR farces having seen a "technical failure" allow a controversial goal to stand in the A League's grand final earlier this year.
VAR is widely expected to be a hot talking point in Russia this summer, with concerns that referees and technology are not ready for such a high-profile debut in FIFA's grand event.
In the 80th minute, Paul Pogba fired France into the lead with a goal that crossed the line off the underside of the crossbar.