Midfielder Mocinic, 21, is set to be replaced in their 23-man squad by Hamburg midfielder Milan Badelj, despite the latter originally ruled out of the squad due to injury also.
The switch is still pending FIFA's approval.
Croatia coach Niko Kovac said Mocinic was sidelined by a problematic ankle.
"I spoke to Ivan Mocinic because he, unfortunately, re-did his injury," Kovac confirmed.
"It's the same ankle, it needs 2-3 weeks recovery and we need to look after the interests of the national team, but also the player and his club and that's why we have to send him home.
"As far as Milan Badelj is concerned, we have sent FIFA documents about the injury and if FIFA approve, Badelj will join us."
If approved, Badelj will join the squad on Friday.
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