The Colombia international was the Eagles’ hero in the 1-0 win over Burnley at Turf Moor, scoring the only goal to hand his team the winning team.
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However, he was not part of Palace squad that picked all points at stake against the Londoners at Craven Cottage.
"His knee. I said to Danny 'sorry, mate, I have to rest you' and that's why he can't play,” Glasner told Sky Sports.
“He knee is a little bit swollen. Of course, we never take any risk, and that's why he misses today's game. We are hopeful that he can return to face City next Sunday."
Despite Munoz’s absence, Crystal Place secured a hard-fought 2-1 win to move to fourth position in the English topflight log.