The company has agreed to pay two fines, one of €5 million and one of €5.5 million, that were imposed in December 2015.
Deutsche Börse said that it "does not share the public prosecutor’s view concerning the accusations raised", but that it has decided to pay the fines to protect the "overriding interests" of the company. Putting the investigation behind it will allow the company to "leave behind the serious burdens placed on it by the investigation proceedings".
Joachim Faber, chairman of Deutsche Börse's board, said: "We did not take this decision lightly. It has been one of the most difficult decisions I have faced together with my colleagues."
The Financial Times has reported that chief executive Carsten Kengeter will personally pay €500,000 as part of the agreement.
Deutsche Börse said in its statement that it "assumes that the current investigation proceedings against [Kengeter] will be closed subject to conditions" and that a decision on Kengeter's contract renewal will be made after all investigations have been concluded.
Financial regulation expert Michael Ruck of Pinsent Masons, the law firm behind Out-Law.com, said: "This is an unusual announcement but one which I am surprised we do not see more of, with firms and others making it clear they do not accept any failings but are making payment of financial penalties to close off such investigations."
"One may question why anyone would do this but given the resources required to contest regulatory investigations or proceedings a commercial and pragmatic view is often required," Ruck said.