Keller, who had been chairman at Freiburg since 2010, was the only name put forward by a DFB commission in charge of finding a new head of the seven million-member association.
He was proposed as the only candidate back in August and on Friday got all 257 votes of the DFB delegates at their general meeting in the capital.
Keller replaces Reinhard Grindel who stepped down in April after coming under pressure over income he received from a DFB subsidiary and a watch he had been given by Ukrainian businessman and soccer administrator Grigory Surkis.
Grindel was the third consecutive DFB president to be embroiled in a scandal after his predecessors Wolfgang Niersbach and Theo Zwanziger were indicted in Switzerland earlier this month over a payment for the 2006 World Cup.
Image credit: Getty Images
The DFB is now hoping Keller, who becomes the 13th president of the organisation, will again steady the ship.
"I am delighted about the clear vote and the faith from the delegates," Keller told the general meeting.
"Those who voted for me voted for change. It is important for me that we lead the DFB into a successful future, with new structures, efficient and transparent."
Keller, an entrepreneur in the field of gastronomy and wine, has also been a member of the German football league (DFL) supervisory board since 2016.