FIFA rejected the Wanderers' appeal after Topor-Stanley was incorrectly sent off during Saturday's 3-1 loss to Cruz Azul in the Club World Cup quarter-final in Rabat.
The Wanderers appealed the first caution by referee Noumandiez Doue, who handed Topor-Stanley a yellow card in a case of mistaken identity after Matthew Spiranovic and Seyi Adeleke were the ones at fault for fouling Cruz Azul striker Hugo Pavone.
"FIFA won't change their decision - we appealed, after seeing the video, knowing it wasn't him, but there's nothing from our point of view we can do now," said Popovic, who will also be without Spiranovic after the Australia international defender was also sent off.
"Nikolai can't play, which is unfortunate. The actual challenge he makes [to earn a second yellow card and hence be dismissed], close to halfway, he makes knowing he can get a yellow if he mistimes it, which in those conditions can happen. He wasn't concerned about that, because he didn't think he had a yellow already.
"So there was confusion throughout, and unfortunately we got the raw end of it. But as a coach, I've moved on from that - after the game I said what I felt.
"We're still at this great tournament, here for a reason as the champions of Asia, and now we have a very difficult game to play."
ES Setif - the fifth African country to be represented at the Club World Cup - were expected to ease past Auckland but Kheireddine Madoui's men were instead eliminated in Rabat.
"I hope we get a positive result. In any case, the experience we will have gained through these matches at the Club World Cup is invaluable," said Madoui.
