The world governing body's settlement with MasterCard brings an end to legal action involving the credit card giant and opens the door for their rivals VISA to sponsor the 2010 and 2014 World Cups.
MasterCard had lodged a claim for £138million in the Swiss courts and the £45million compensation deal includes £15million to settle previous action brought by the company in a trademark dispute over FIFA's use of twin globes.
It is understood that the trademark dispute prompted FIFA officials to court VISA instead, but a US federal court last December ruled FIFA executives had "lied repeatedly" in negotiations with MasterCard.
FIFA president Sepp Blatter said: "FIFA has, first of all, resolved a problem.
"Secondly - much more importantly - has paved the way to a good, new partner that will support it and its manifold activities efficiently all around the world."
Blatter told delegates at the FIFA Congress last month that the compensation would not affect the financial support for national associations and confederations.
FIFA have also reinstated marketing chief Jerome Valcke who was sacked in December following the court hearing. An appeal court last month ordered a review of the December hearing and FIFA insist that means the original ruling about his misconduct has been voided.