Ludogorets, who won their maiden league title in May, said club officials were the victims of racial abuse and offensive chants while cups of beer and other objects were thrown at them in the main stand of Maksimir stadium.
Croatian champions Dinamo won the second qualifying round tie 4-3 on aggregate after they scored in the eighth minute of stoppage time to win the second leg 3-2. A draw in that match would have sent the Bulgarians through on away goals.
"Dinamo are to face charges for improper conduct by their supporters," said UEFA in a statement, adding that the disciplinary board would hear the case on Aug 23.
Razgrad-based Ludogorets, whose protest was backed by the Bulgarian Football Union, were also angry at the performance of German referee Felix Zwayer.
Dinamo beat Molodvan champions Sheriff Tiraspol 1-0 away in the first leg of the third qualifying round on Wednesday.