The financial services firm will receive the payment and scrap its sponsorship of the 2010 and 2014 FIFA World Cups.
The row exploded when FIFA offered MasterCard’s arch-rival Visa the sponsorship rights to the two tournaments. MasterCard insisted a first-right of refusal option had not been offered to them and took soccer’s world governing body to court.
At the end of last year a US judge ruled FIFA had not honoured its agreement with the firm which has been a major sponsor since 1994.
The $90m from FIFA – paid in instalments – is compensation for MasterCard for the discontinuation of their sponsorship agreement.
FIFA confirmed last night they are ‘set to implement a contract’ with Visa after the MasterCard deal was finalised.
FIFA president Sepp Blatter said: “FIFA has, first of all, resolved a problem and, 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.”