The technology, developed by Germany-based company GoalControl and making its debut at the 2014 World Cup, was required for the first time in the 48th minute of the Group E encounter.
Karim Benzema's initial shot struck the inside of the post and bounced across the goal, where it hit Noel Valladares and rolled over the line before the Honduras goalkeeper hooked the ball back out.
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The system correctly awarded a goal to France but caused confusion in the stadium and around the world by first homing in on the ball striking the woodwork and flashing up a "no goal" sign.
FIFA on Monday said the animations that appear on TV and stadium screens are generated automatically, but said it is working with GoalControl to tweak the system to remove any ambiguity in future.
"Everything worked according to plan," FIFA's head of media Delia Fischer told the press during a briefing at the Maracana. "The animations provided additional support because the live action was not conclusive [over whether the ball had crossed the line].
"Yesterday’s situation was quite unique. As the replays are automatically triggered, you saw first the ‘no goal’ and then the ‘goal’ sign. What we are doing is working to make it even clearer and to change it so you only see the ‘goal’ sign in situations like yesterday’s [from now on]."