Three minutes into the second period, the German-manufactured GoalControl system was called into action when a volley from Karim Benzema, who ended the night with two goals, came back off the post.
It bounced back into the area before hitting Honduras goalkeeper Noel Valladares with the ball then diverted back towards the goal.
The keeper tried to scoop the ball to safety, but Brazilian referee Sandro Ricci awarded the goal -- classed as an own-goal -- after consulting the instant technology.
France, whose 2010 World Cup was a footballing and public relations disaster, dominated the Group E match, twice hitting the woodwork in the first half.
First, Blaise Matuidi fired the ball towards the target but Valladares saved well and pushed the ball on to the crossbar.
Then, on the 23 minute mark, Antoine Griezmann, selected ahead of Olivier Giroud, climbed above the defence but headed on to the bar.
Stoke City midfielder Winston Palacios was yellow-carded for a brutal stamp on Pogba with the Frenchman also booked for a retaliatory kick.
Palacios was then red-carded in the dying moments of the half for another foul on Pogba inside the box.
Benzema converted the resulting penalty for his seventh goal in his last seven internationals.
The Real Madrid striker then played the crucial role in his team's historic second goal before striking his second of the night from a tight angle in the 72nd minute.
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