Ludogorets, who won their maiden league title last season, 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 the Maksimir stadium.
The Bulgarians, knocked out 4-3 on aggregate, also accused German referee Felix Zwayer of favouring their Croatian opponents.
Ludogorets said their Brazilian midfielder Marcelinho was wrongly sent off 12 minutes after the break while Dinamo's Sammir should have received a red card for elbowing an opponent a few minutes later.
The team, who have received the backing of the Bulgarian Football Union (BFU), also said Zwayer unnecessarily added eight minutes of injury time.
"The BFU respectfully insists UEFA ... instigate disciplinary proceedings against Dinamo ... on the basis of a protest that has been lodged by Ludogorets," the BFU said in a letter sent to European soccer's governing body.