The league said Thursday that it turned down the request from Cologne. It said transfer deadlines "are binding for all clubs" and help protect the integrity of competitions.
The contract between Choupo-Moting and struggling Cologne arrived at the DFL 12 minutes after the winter transfer window closed.
Choupo-Moting picked Cologne over West Bromwich Albion with a half-hour to spare. But when his father and agent tried to fax the contract, the connection broke down.