The simple answer to this is that Admiral Donitz was not punished for the German use of unrestricted submarine warfare. While he was found guilty of breaching international law by doing so, no sentence was given for this. This was justified by the fact that both the Royal Navy and United States Navy had similar policies on submarine warfare. However, his use of unrestricted submarine warfare was just one of four charges levelled against Donitz. The other areas were breaches of international law that no other Allied nation carried out. Donitz was charged with allowing the 'Commando Order' to be put into force by the German Navy (which called for the execution of Allied POWs in some circumstances), allowing the use of slave labour in German shipyards, and not fully arguing against Hitler when he proposed ignoring the Geneva Convention (though there were mitigating circumstances on this last charge). Donitz was found guilty on these charges, and sentenced to imprisonment.

Erich Raeder, who was in charge of the German Navy until January 1943, was also tried at Nuremberg. He too was charged with allowing unrestricted submarine warfare, and like Donitz was found guilty but not sentenced on the same grounds. However, he would be sentenced for his role in covering up the circumstances surrounding the sinking of the liner Athenia in September 1939. Raeder was also charged with evading the terms of the Versailles Treaty, and carrying out an aggressive war, especially given his role in planning for the invasions of Norway and Denmark. Like Donitz, Raeder would be charged with implementing the Commando Order in the German Navy. He was found guilty on these counts and sentenced to imprisonment. He would request that his sentence be increased to the death sentence, as he believed he would die in prison, but this request would be denied, as the court did not feel it could increase its sentences.