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New York Yankees designated hitter Alex Rodriguez (13) prior to a game against the Miami Marlins at Marlins Park. Reuters

The New York Yankees and Alex Rodriguez have come to a settlement over disputed bonus money, agreeing that $3.5 million will be donated to a range of charities. The dispute came after Rodriguez hit his milestone 660th home run -- tying Hall of Famer Willie Mays on the career list -- and his contract called for a $6 million payout.

The Yankees argued that it had the discretion to not make the payment, and it was rumored before the season that the franchise would not pay "A-Rod" after he hit the milestone. The $6 million payout was supposed to be given in exchange for merchandise marketing rights, which the club reportedly argued no longer had value because of A-Rod's use of performance-enhancing drugs. The club's stance led to a possible grievance by the Major League Baseball players' association, according to the Associated Press.

The relationship between the famous designated hitter and Yankees' brass deteriorated after Rodriguez was targeted by the MLB's Biogenesis drug investigation and was suspended for the entire 2014 season. Rodriguez in turn sued MLB, the players’ union and the Yankees’ team physician.

MLB released a statement Friday saying that Rodriguez and the Yankees have "amicably resolved" their potential dispute. The agreement said that $1 million will go to charities long-supported by either the player or franchise, naming the Special Operations Warrior Foundation, the Boys & Girls Club of Tampa (where the Yankees hold spring training) and Pitch In For Baseball. The remaining $2.5 million will go to the MLB Urban Youth Foundation, which will "use the money to further programs and initiatives aimed at increasing youth participation in baseball, particularly in urban areas," the statement read. MLB Commissioner Robert Manfred, Jr. will determine which initiatives are given a portion of the remaining $2.5 million after consulting with Rodriguez.

Under Friday’s agreement, Rodriguez reportedly doesn't see a cent of the bonus that was included in his 10-year $270-million contract signed with the club in 2007. The Yankees also save $4.9 million under the agreement, $2.5 million of which is from the difference from the original $6 million payout and the $3.5 million in donations. The club saves an additional $2.4 million more in luxury tax because Rodriguez will not directly receive any money, the AP reported.