Croatian Foreign Minister Tonino Picula has cancelled a visit to Montenegro after the Croatian embassy in Serbia, Montenegro's sister republic, was attacked by demonstrators on Sunday.
Anger was apparently prompted by TV pictures of the match
The protesters, who were celebrating a win by the Serbia and Montenegro team over Croatia at water polo, broke windows at the embassy and replaced the Croatian flag with a Serbian one.
The incidents were preceded by violence at the match itself, which was held in Slovenia.
Disgruntled Croatian fans fought Slovene police, damaging the sports venue in the city of Kranj and beating journalists.
At least 13 fans were arrested following the incidents in Kranj, in which two people were reported to be seriously injured.
Croatian Prime Minister Ivica Racan described the fans as vandals who had brought shame on their country.
Responding to the Belgrade riots, Foreign Ministry spokeswoman Natalja Bukovec said Mr Picula's visit could not be carried out under such circumstances.
She added that Croatia had made an official protest to the ambassador of Serbia and Montenegro, Milan Simurdic.
At least 13 Croatian fans were arrested in Slovenia
Celebrations after Serbia and Montenegro's 9-8 win in the final of the European championships began peacefully in Belgrade's main square, with several thousand fans waving flags and setting off firecrackers.
But some elements in the crowd, apparently enraged by television pictures of the clashes in Kranj, marched on the Croatian embassy and threw stones and other objects at the building.
One group climbed onto a balcony, dismantled the Croatian coat-of-arms and replaced the flag.
Police said 38 people were arrested during the riots.
Violence also broke out in Novi Sad, Serbia's second city, where several hundred fans smashed town hall and shop windows, including those of the local McDonald's restaurant.
They sprayed nationalist graffiti, including the names of Serb leaders suspected of committing war crimes in the conflicts in Bosnia and Croatia.
Local hospital sources reported that 20 people were injured including five policemen, and one man received gunshot wounds in the stomach.
Correspondents say relations between Serbia and Croatia, which have been warming recently, are unlikely to be seriously affected by the incidents.
However, tensions remain from the 1991-95 war, when ethnic Serbs in Croatia fought against Zagreb's secession from the old Yugoslav federation.