The criminal investigations ended with the conclusion that MF Global employees did not intentionally break the law. Just last year, Mr. Corzine settled much of the private MF Global litigation. And a trustee has long recovered the missing customer money (much of it wound up at MF Global’s banks and clearinghouses) and made whole the farmers and hedge funds whose accounts were raided in the firm’s final days.

In a statement on Thursday, Mr. Corzine said, “As the C.E.O. of MF Global in 2011, I have accepted responsibility for its failure, and I deeply regret the impact it had on customers, employees, shareholders and others.” He added: “I remain gratified that several years ago all customer money was recovered and returned to MF Global customers.”

His lawyer, Andrew J. Levander, said: “Mr. Corzine has given more than 10 days of testimony under oath, and these matters have been investigated exhaustively by two U.S. attorney’s offices, the F.B.I., the S.E.C., the C.F.T.C., Finra and Congress.” (Finra is the Financial Industry Regulatory Authority.)

And yet, Mr. Levander said, “None of these investigations have led to allegations that Mr. Corzine engaged in any kind of intentional misconduct or fraud, or that he was at any time not truthful in his many hours of testimony.”

The case also concludes a long-running political challenge for the commodities agency, which came under fire for not preventing a breach of customer money at a firm it regulated. Compounding the pressure, Mr. Corzine was a sensitive target, a prominent Democrat who has been a confidant of leaders in Washington and on Wall Street.

Against that backdrop, the agency extracted the $5 million payout from Mr. Corzine, a sum far greater than what it could have expected to win if he had been found liable at trial. During negotiations with Mr. Corzine last year, the commission also strengthened aspects of the deal after some of the agency’s commissioners questioned it, The New York Times reported at the time.