The blunder has raised doubts over whether Poll will continue to referee at the tournament, even though at one stage he was tipped to referee the final.
Blatter could not understand how the four officials who were all connected via radio were unable to communicate with each other to resolve the mistake.
"An error of this kind should not happen when there are four people in the team," Blatter told a press conference in Germany.
"What is incomprehensible is that no-one intervened. I cannot understand it, it is like a blackout.
"One of them should have intervened and run on the field and said 'stop, stop'.
"I place my trust in the referees committee. I think they have enough tact to deal with this case."
The FIFA boss did praise Poll for earlier efforts.
"We should not forget that Graham Poll in his previous matches achieved fantastic things.
"We cannot excuse it but we should understand it. Referees are human beings and human beings make errors."
Had Croatia scored with the twice booked Simunic on the field, the match may have needed to be replayed.