The US striker's omission comes amid uncertainty over his future after the collapse of his proposed transfer to Everton this week. Balogun was close to joining the English club for a reported £40 million, but opted to pull out of the deal due to concerns over his health in a medical examination.
Monaco are under pressure to sell Balogun or another top player to generate money and comply with the French league's financial rules. The club's sporting director, Thiago Scuro, has stated that it is still possible to sell the striker's contract to a league where the transfer window remains open. One such option is the Saudi Pro League, where the window closes on October 12.
Monaco begin the league phase of the Conference League on October 15, and Balogun's name did not appear on the club's provided squad list published by UEFA late on Thursday.