Trailing after strikes from Fedor Smolov on 22 minutes and Joaozinho, 11 minutes later, the 26-year-old Balotelli slipped as he struck a curling shot home in the 43rd minute before bending over to cough and retch.
It was Balotelli's fifth goal in four games for Nice after twice bagging braces in Ligue 1 wins over Marseille and Monaco.
The Italian striker, having been in some distress, was replaced at half-time
Nice lost their first Europa League Group I game 1-0 to Schalke 04.