He was the second high-ranking official following former President Wolfgang Niersbach to step down over a scandal involving a payment to world soccer's governing body FIFA allegedly to ensure the 2006 World Cup was awarded to Germany.
FIFA is due to elect a new President later on Friday.
The DFB is set to present an independent report it commissioned into the affair next week. It will elect designated successor Reinhard Grindel as its new president in April.
"For the good of our football and the DFB it is necessary to make a completely new start in a credible and consequent manner, even in matters of personnel," Sandrock said in a DFB statement.
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"It is just good style and normal to give a newly elected president of the DFB the chance to propose a new General Secretary for election."
The scandal has also involved former World Cup-winning coach and player Franz Beckenbauer, who headed the 2006 World Cup organisation.
Niersbach resigned as DFB president late last year after failing to explain why the 6.7 million euro ($7.38 million) payment was made to FIFA.
Beckenbauer has said it was to unlock a bigger payment from FIFA and has denied any wrongdoing.
"Helmut Sandrock has been a reliable partner, especially in this difficult time," said interim DFB President Reinhard Rauball.
Sandrock, tournament director for the 2006 World Cup, had been General Secretary since 2012, taking over from Niersbach.
He also worked for FIFA as general coordinator of the club World Cup in Japan in 2008 and he represented the organisation at the 2010 World Cup and 2009 Confederations Cup.
The DFB-commissioned investigation is not the only one, with Swiss and German prosecutors also looking into the affair.
Frankfurt's state prosecutor has formally launched an investigation into Niersbach and two other former World Cup 2006 officials over tax evasion in relation to the payment.
($1 = 0.9079 euros)
(Reporting by Karolos Grohmann, editing by Ed Osmond)
