New York — Alex Rodriguez had his own personal doubleheader Friday, first with an agreement that gave him possession of the baseball he smacked for his 3,000th hit and then with a deal that resolved his longstanding dispute with the New York Yankees over a $6 million home run bonus. In both cases, the biggest beneficiaries will be designated charities.

First, the baseball. About 90 minutes before Friday night’s game in the Bronx against the Tampa Bay Rays, Zack Hample, the fan who grabbed Rodriguez’s 3,000th hit after it soared into the right-field stands for a home run at Yankee Stadium on June 19, pulled the ball, secured in a Ziploc bag, from a black backpack and handed it to Rodriguez, who said he would give it to his daughters.

In exchange, the Yankees assured Hample, who has achieved some fame for snaring baseballs hit into the stands, that they would donate $150,000 to a charity, Pitch In for Baseball, that aims to distribute baseball equipment to deprived areas in the United States and abroad. The Yankees said Hample had supported the charity for years.

In the immediate aftermath of Rodriguez’s 3,000th hit, Hample rebuffed efforts by two of the Yankees’ top executives — Randy Levine and Lonn Trost — to strike a quick agreement to give the ball to Rodriguez and left open the possibility that he might just choose to sell it. Still, he indicated he could also change his mind and reach a deal with Rodriguez and the Yankees, and now he has.

Recalling one of his initial discussions with Levine that turned the tide of negotiations, Hample said, “He told me, ‘If it would help you make a decision with the baseball, the Yankees might consider making a sizable donation to the charity.’”

Hample also received two signed black bats, one inscribed, “Nice catch,” and a jersey autographed by Rodriguez. Hample apologized for a derogatory comment he made about Rodriguez on Twitter.

Rodriguez, who massaged the ball in his right hand, forgave Hample. “I have a Ph.D. in saying some dumb things over the years,” he said.

Now, the bonus. The Yankees and Rodriguez originally had an agreement that he would receive a series of $6 million bonuses as he reached the career home run milestones of Willie Mays, Babe Ruth, Hank Aaron and, finally, Barry Bonds.

But in the wake of Rodriguez’s yearlong drug suspension in 2014, the Yankees changed their minds. They contended that the bonuses were not part of his current 10-year contract with the team, which was reached in 2007, but instead represented a separate marketing deal that was rendered moot when Rodriguez’s image was damaged by his links to performance-enhancing drugs.

Rodriguez, the Yankees argued, was no longer marketable. Thus, when Rodriguez hit his 660th home run, tying Mays, no money was forthcoming. The fact that the home run broke a 2-2 tie in the eighth inning of a game against the rival Boston Red Sox and came in front of a capacity crowd at Fenway Park did not matter, either. No bonus, the Yankees said.

Or, as Yankees general manager Brian Cashman put it to reporters the day after Rodriguez’s Boston heroics: “We have the right but not the obligation to do something. And that’s it. It’s not ‘You do this, you get that.’”

Rodriguez, who has had a surprisingly strong comeback season at age 39 and has diligently avoided creating any new disputes with the Yankees, did not lash out when the bonus was withheld. On Friday, he said he entered spring training with a commitment to himself to keep his head down, let his bat do the talking and help the team win as many games as possible.

Or, as he put it to reporters just hours before he hit his 660th: “I’ve learned my lesson. I’m doing things a different way now. I know these things will work themselves out.”

And now, they apparently have. A deal has been struck in which Rodriguez and the team have agreed that in lieu of the $6 million bonus being paid to Rodriguez, $3.5 million in contributions will be made by the Yankees to several charities: the Special Operations Warrior Foundation, the Boys & Girls Club of Tampa, Florida, Pitch In for Baseball and the MLB Urban Youth Foundation.

“I just thought it was important to do the right thing,” Rodriguez said. “Like Zack, I was thinking long and hard about doing the right thing, doing something important for a lot of people, and turning a negative situation perhaps into a positive one. I think we all did the right thing.”