Juergen Fitschen and Anshu Jain resigned during an emergency meeting of the bank's supervisory board on Sunday.
The bank has been hit by a series of scandals recently, including a $2.5bn (£1.7bn) fine for its part in rigging the Libor inter-bank lending rate.
Mr Jain will be replaced by John Cryan, who will become sole chief executive when Mr Fitschen leaves in May 2016.
Deutsche Bank is also paying $55m (£35.7m) to settle civil charges for allegedly mis-stating financial reports.
As well as legal and regulatory issues, the management changes follow disappointing financial performance at the bank.
Net income for the first three months of 2015 halved to €559m compared with the same period a year earlier.
This is despite revenue rising by almost a quarter to €10.4bn.
Shares in Deutsche Bank have jumped 6% the day after the German banking giant's co-chief executives resigned.