On Tuesday, UEFA announced Union - who are playing their first season in the Europa League - would be fined €40,500 (£35,600) for their away game at Braga and 12,000 euros for their home match versus Union Saint-Gilloise.
More fines and further penalties are expected for both Union Berlin and Malmo after Thursday's fixture, where both sets of fans threw fireworks onto the pitch, causing the game to be delayed for 20 minutes.
The two clubs play each other in the return fixture in Berlin on Thursday.
After the Malmo game, Union President Dirk Zingler said the fan behaviour was "unacceptable", adding "we don't do (things like) that - and then suddenly we do."
Manager Urs Fischer was even more scathing.
"All I can say about the incidents is that I absolutely cannot understand it and something like that has no place in football. It is shameful."
No timeline has been laid out for when additional fines may be levied.
Union Berlin, who are top of the Bundesliga after nine games, sit third in their Europa League group after one win and two losses.
