The Manchester City midfielder injured his shoulder with his failed attempt during his side’s win in Serbia on Wednesday.
Nunes was handed his 10th start of the season by Pep Guardiola for City’s final Champions League group stage match.
However, he was almost forced off just minutes into the second half.
The Portugal international appeared to injure his shoulder attempting an overhead kick.
He stayed down in agony afterwards and received treatment from the club’s medical staff before continuing,
Concerned supporters were quick to react to the incident on social media.
One fan wrote: “Matheus Nunes that was unnecessary.”
Another added: “Please don’t break yourself Matheus Nunes.”
Meanwhile, a third supporter also commented: “Matheus Nunes is the type of guy to get injured while attempting a bicycle kick.”
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Nunes was a standout performer for City, setting up Micah Hamilton’s debut goal to open the scoring.
Fellow youngster Oscar Bobb later doubled the visitor’s lead before Kalvin Phillips’ penalty sealed a 3-2 victory, despite a late fight back from Red Star.
City were already confirmed as group winners before Wednesday’s match, having won all of their matches in group G.
As for Nunes, the 25-year-old completed a £47million move to the Etihad Stadium from Wolves in the summer.
He has since provided three assists in 13 appearances across all competitions so far this season.