On June 22, 1941, Nazi Germany began its invasion of the Soviet Union. With the Soviet troops in a rout, the NKVD began executing its political prisoners as they retreated. On the night of 24/25 June 1941, Petronaitis was taken to a forest near Rainiai and, together with 77 other political prisoners, was tortured, murdered, and buried in a mass grave. On exhumation three days later, his body was difficult to identify as it had been disfigured by the tortures applied to it.