Swedish media reported that Union Berlin supporters threw fireworks onto the pitch shortly after the second half started and Malmo supporters responded by throwing a flare.
Reuters has contacted European football's governing body UEFA for comment on the incident.
The game resumed and ended in a 1-0 win for Union Berlin after Sheraldo Becker scored in the 68th minute.
Malmo are bottom of Group D with no points after three games, while Union are third with three points.