During the German invasion of the Soviet Union in 1941, Rall was appointed commander of the Eastern defensive position on 25 June and oversaw the installation of shore batteries on the islands of Bolshoy Tyuters and Lavensaari, and the laying of minefields in the Gulf of Finland. He was then tasked with taking part in the complicated operation to evacuate the ships of the Baltic Fleet from besieged Tallinn and bring them to Kronstadt. Rall was given command of the rearguard. With three evacuation routes possible, Rall advised taking the southernmost one. Though this passed through shallow water and along 200 miles of occupied coastline with enemy shore batteries, Rall pointed out that the shore batteries mainly consisted of light field guns, which could easily be suppressed by Soviet naval artillery, and that 200 vessels had made the passage without difficulty. The advice was rejected by Marshal Kliment Voroshilov, commander of the Leningrad Front, who, concerned about the possibility of Latvian and Estonian crews, and even Soviet sailors, defecting to the enemy, ordered Rall and his superior Admiral Vladimir Tributs to take the middle route, despite it having been heavily mined by enemy forces. The evacuation convoys soon began to suffer heavy losses to mines and air attacks. Rall's flagship, the destroyer "Kalinin", struck a mine and began to sink. The destroyer "Volodarskiy" came alongside to take off the crew, but also hit a mine and sank. Rall, injured and concussed, was taken aboard a cutter. He was eventually brought back to Kronstadt with the survivors of the evacuation force. While the Soviet leadership claimed a victory in evacuating a number of troops and refugees, Rall remarked that it had been a "Second Tsushima", referring to the heavy defeat at the Battle of Tsushima during the Russo-Japanese War.