In the autumn of 1944, the SS proceeded to gradually eliminate Sonderkommando prisoners. The first 200 Sonderkommando prisoners were murdered in September. On 7 October 1944, camp authorities planned to eliminate a subsequent group of prisoners, but this time the Sonderkommando resisted. During the revolt, Sonderkommando rebels gathered in the crematorium IV forecourt, attacked the SS guards and set fire to the undressing room inside the building. Then armed SS units arrived and opened fire on the rebels, killing most of them in the crematorium courtyard. Once the revolt was quelled, the SS conducted a selection among the surviving Sonderkommando prisoners. Afterwards some of them were forced to lie on the ground and then executed with a shot in the back of the head. A group of Sonderkommando prisoners from crematorium II also joined the revolt started near crematorium IV. Three of the prisoners tried to blow up the crematorium furnaces, though they unfortunately failed. A remaining group of prisoners (approximately 80) cut through the barbed wire fences enclosing of the crematorium as well as the adjacent women’s camp and fled in a southerly direction. SS units gave chase and caught up with them some 1.5 km from the crematorium, therefore still within the concentration camp zone (Lagerinteressengebiet). The fugitives were shot dead with machine guns.

As an immediate result of the revolt, three SS guards and 450 Sonderkommando prisoners were killed. The SS next conducted investigations to eradicate the resistance movement within the Sonderkommando and identify the prisoners employed in the Union factory who supplied the explosives. Consequently, over a dozen Sonderkommando prisoners as well as female prisoners employed in the munition factory were arrested. The Sonderkommando members were murdered in Block 11, whereas the women, Ella Gartner, Róża Robota, Regina Safirsztajn and Estera Wajsblum, were publicly hanged in early January 1945.