Home fans at the Stade Velodrome on November 5th had set off flares, thrown projectiles and used lasers.
UEFA fined Marseille 71,000 euros (£62,800) and ordered them to close a part of the south stand for the Champions League match against Newcastle on November 25th.
Goalkeeping coach Alexandre Salvat was given a two-match ban for insulting an official during the Atalanta match.