Derek Jeter has won the auction for the Marlins for $1.2 billion and will serve as the franchise’s CEO, a source with direct knowledge of the situation said.

The former Yankees captain and future Hall of Famer will oversee both baseball and business operations, sources said. He also will have a large voting stake in team affairs, roughly 20 percent. Billionaire money manager Bruce Sherman will be the controlling owner.

“It’s a deal,” the source said. “The ink is dry.”

As principal owner, Sherman is investing several hundred million in the acquisition and Jeter less than $30 million, sources said.

Sherman, who lives in Naples, Fla., did not know Jeter until he found out the retired Yankee was bidding for the Marlins and inquired months ago about joining his group, sources said.

In the past, Sherman had unsuccessfully bid for a minor league baseball team.

In the following months, Sherman outlasted other billionaire Jeter backers such as Richard Chaifetz and Quogue Capital Founder Wayne Rothbaum, who eventually left Jeter and formed his own rival Marlins bidding group with Tagg Romney, the source said. Sherman then became the lead of Jeter’s bidding group.

Like his friend and mentor, basketball great Michael Jordan, Jeter is first becoming a top sports team executive with the goal of learning the business, then buying a franchise, a source who knows Jeter said. Jordan, a Marlins co-investor in the Sherman/Jeter bidding group, first ran the NBA’s Wizards, then became owner of the Bobcats (now the Hornets).

Jeter, who retired from the Yankees following the 2014 season, does not have any baseball management experience and previously had teamed with former Florida governor Jeb Bush in an attempt to purchase the Marlins, but that pairing fell apart in May.

When it appeared Jeter and Bush were on their way to winning the bid at Jeter’s jersey-retirement ceremony in The Bronx earlier that month, Jeter downplayed any potential role in the sale of the team.

“There’s nothing to report on that,” Jeter said. “Absolutely nothing. I think sometimes [with] stories, people get ahead of themselves. And there was a story people got way ahead of themselves a few weeks back. There’s nothing to report. If there’s something to report, I’ll let you know.”

At the time, though, his friend and former teammate Jorge Posada said he believed it would be a good move.

“People are asking, ‘Is it going to happen?’ That would be great,” Posada said. “He brings that winning mentality. The people in Miami want it. They want change.”

During his on-field speech May 14, Jeter repeatedly mentioned the importance of the Yankees franchise to him.

“I’m eternally grateful to be part of the Yankee family,” Jeter said.

The 69-year-old Sherman plans to maintain his Marlins ownership for years to come, then eventually turn the team over to his children, sources said.

He made much of his fortune when Legg Mason bought his Private Capital Management money management firm, based in Naples, Fla., for $1.4 billion in 2001.

Sherman became best known for being a big investor in newspapers.

Sherman’s Private Capital Management fell in size by the time he retired in 2009 from its $30 billion peak to $2.4 billion in assets.

When Sherman was riding high, he said he liked investing in cash-rich companies because they could buy back shares or make investments to improve their share prices, according to the 1999 book “Investment Gurus: A Road Map to Wealth from the World’s Best Money Managers.”

The Marlins do not fit the typical Sherman criteria, as they are expected to lose $70 million this year.

Sherman did not grow up wealthy, being raised in middle-class Douglaston, Queens.

— additional reporting by Joel Sherman