The Wanderers were just two minutes away from a dream tie against Real Madrid when things fell apart on Saturday.
The Mexican side were awarded two penalties – the first sent the match to extra time – by Ivorian referee Noumandiez Doue while both Matthew Spiranovic and Nikolai Topor-Stanley were given red cards as the Wanderers succumbed 3-1.
Not helping either side's cause was a waterlogged pitch due to a torrential downpour throughout the night in Rabat.
"I have played in conditions like that before but you wouldn't expect it in a tournament like this," Popovic told Fox Sports.
"You expect the very best and the best officials as well but I think some of them were here on work experience tonight.
"Unfortunately we paid the price. It's a tough one to take. With two minutes to go we were so close to getting that dream game."
Instead of facing the likes of Cristiano Ronaldo and Gareth Bale, the Wanderers will instead have to pick themselves up for a fifth-placed play-off against African champions ES Setif on Wednesday.
Despite the heart-breaking nature of their defeat to Cruz Azul, Popovic had nothing but praise for his side.
"The players gave their all," he said.
"Everything went against them but I'm very proud of them tonight.
“The pitch was appalling. The officiating, I probably can't say what I really think of that … it was never going to be for us tonight."
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