The two clubs had been embroiled in a bitter feud over the 17-year-old after Le Havre accused United of offering financial inducements to tempt Pogba into breaking his contract.
United have always denied that, citing the fact Pogba did not have a deal in place, and they were backed by FIFA who allowed them to register the youngster in October 2009.
Le Havre threatened to take the matter further but both clubs have now confirmed that all outstanding issues have been resolved.
A statement on manutd.com read: "Le Havre AC and Manchester United FC are pleased to announce that following discussions between the two clubs, an agreement has been reached in relation to the registration of Paul Pogba with Manchester United in July 2009.
"The terms of the agreement will remain confidential.