Fans of PSV ripped up seats and lit flares, throwing one towards Arsenal supporters during the game at the Emirates, which ended in a 1-0 win for the hosts.
PSV were also issued a fine of €40,000.
PSV's next away game in European competition comes against Norway's Bodo/Glimt on Nov. 3.
UEFA added that PSV must "contact Arsenal within 30 days for the settlement of damages caused by its supporters, i.e. for the damaged seats."
PSV face Arsenal at the Philips Stadion later on Thursday. Arsenal lead Group A on 12 points from four games, five ahead of the second-placed Dutch side.