Bierhoff had been working with the German FA since 2004 and played instrumental roles in their 2014 World Cup triumph and 2017 FIFA Confederations Cup victory.
But Germany have failed to convince in their last three major tournaments and Bierhoff's decision to step down could be the first among a number of major reshuffles that could hit the association's hierarchy.
A 2-1 defeat to Japan, 1-1 draw with Spain and a 4-2 victory over Costa Rica were not enough to secure passage to the round of 16.
“I’ve told German FA president Bernd Neuendorf of my decision today,” the 54-year-old wrote in a personal statement.
“I’m clearing the path for setting a new course.”
“My work was founded upon the conviction of doing my best for the German FA and the national teams. But that only makes the results of the men’s national team at the World Cups in Russia and Qatar more painful. That’s why I’m not leaving without the necessary self-criticism.
“We didn’t manage to repeat previous successes and to give supporters reason to cheer in the last four years. Some decisions we had been convinced of turned out wrong. No one regrets that more than me. I take responsibility for that.”
DFB president Bernd Neuendorf said: "Oliver Bierhoff has rendered great services to the DFB. Even if the last tournaments fell short of the sporting goals, he stands for great moments.
"His work will always be linked to the World Cup success in Brazil. Even in turbulent times, he always pursued his goals and visions and left a lasting mark on the DFB.
"On behalf of the DFB employees, I would like to thank Oliver Bierhoff for everything he has done for us and for football in Germany."
