World soccer's governing body said Tuesday the incident had been spotted by the fourth official without using a monitor, who then alerted referee Horacio Elizondo through their communications system.
"FIFA will open a disciplinary investigation into Zidane's conduct to enable it to clarify the circumstances surrounding the incident as exactly as possible," FIFA said in a statement.
Zidane and Materazzi exchanged words after Italy broke up a French attack in extra-time of Sunday's final in Berlin. Seconds later, Zidane lowered his head and rammed Materazzi in the chest, knocking him to the ground.
Zidane was sent off, reducing France to 10 men. Italy won the game in a penalty shootout.
Referring to Zidane being voted the player of the tournament by journalists, FIFA said the ballot boxes remained open at the main media center in Berlin until midnight on Sunday. The game was over by then. "It is impossible to determine how many journalists cast their votes before the match and how many during it, as the ballot papers were not counted until after the deadline for voting had expired," FIFA said.
Materazzi admitted he insulted Zidane before the France captain head-butted him, but denied calling him a "terrorist."
"I did insult him, it's true," Materazzi said in Tuesday's Gazzetta dello Sport. "But I categorically did not call him a terrorist. I'm not cultured and I don't even know what an Islamic terrorist is."
The 32-year-old Inter Milan player did not elaborate exactly on what he said to Zidane.
"It was one of those insults you're told tens of times and that always fly around the pitch," he said.