Balotelli, who made a quick impact after joining Milan from Manchester City in January, went off near the end of Milan's friendly against Los Angeles Galaxy in the United States which the Serie A side won 2-0 on Wednesday.
"During the course of the game, Mario Balotelli suffered a muscular problem in his right thigh," said AC Milan in a statement. "He will be examined on his return to Italy."
The seven-times European champions will discover their opponents for the two-leg playoff round tie when the draw is made at UEFA headquarters on Friday. The first leg will be played on August 20 or 21 with the return one week later.
Milan finished third in Serie A last season but only the top two Italian sides qualify directly for the group stage.
Balotelli could also be ruled out of Italy's friendly at home to Argentina on Aug. 14.