"We are aware of the reports and we have started disciplinary proceedings," a FIFA spokesman told Reuters.
Greece won the match 2-1 in Heraklion last Wednesday thanks to a second-half penalty by Giorgios Samaras.
Football's world governing body said it was probing reports that local fans aimed the infra-red beams at Aouate as he was preparing to face the penalty that kept Greece top of Group Two and damaged Israel's chances of qualification.
"I certainly was blinded during the penalty but it did not affect me not stopping it," Aouate told Israeli army radio.
"In the first half I was being blinded and I alerted the referee. In the second half they (the fans with the laser) moved from one end of the stadium to the other so that they could continue to blind me."
The Swiss won the game 2-1, but the distracting beams were directed at striker Alexander Frei as he was taking a penalty for Switzerland's opening goal.
"We have not been officially informed by FIFA over this," a Greek FA official told Reuters. Another official said the FA was aware of Israeli media reports on the issue.
Israel FA spokesman Gil Levanoni said his organisation was "awaiting the outcome of FIFA'S investigation but we are not getting involved in the matter at this time."
