Kopeć's work was cut short due to his arrest by the Gestapo in 1940 together with his daughter Maria and son Stanisław in an operation against a Polish Underground State-run secret university. He was imprisoned at the Pawiak prison in Warsaw and executed by the Germans in 1941 at Palmiry, near Warsaw, together with his son, as a reprisal for an action of the Polish resistance, as a part of the German AB-Aktion in Poland. The University of Wrocław named its annual International Conference on Arthropods the Stefan Kopeć Memorial Conference in Kopeć's honor.