Karim Benzema scored the first and third goals for Brazil, but the problem arose when Noel Valladares pushed the ball marginally over his own line to make it 2-0 after the Real Madrid striker had struck a post.
The goal-line technology system initially displayed the words 'no goal' - in reference to the effort that hit the post - before awarding the goal after Valladares' touch.
The sequence of events caused confusion among some fans and commentators, and FIFA have promised to take action.
"We are working to make it even more clear and will modify the guidelines so that you just see the goal," FIFA spokesperson Delia Fischer is quoted as saying in a media briefing.
"There was no mistake but we will modify the guidelines to make it even more clear for the viewers in the stadium and on TV.
"Yesterday's situation was quite unique as the ball hit the inside of the post, rebounded away from goal before hitting the goalkeeper and rolling across the goal-line."
