The NFL team's president Paraag Marathe has joined the Championship outfit's board of directors as a result of the agreement.
Leeds owner Andrea Radrizzani will continue to serve as chairman and majority shareholder following the deal.
"This strategic partnership enables Leeds United to align with and gain invaluable expertise from the owners of one of the biggest global sports entities," Radrizzani said in a statement on the club's website.
"The 49ers are an innovative, successful organisation and we are delighted to have access to such a rich source of business and sporting expertise."
Leeds have confirmed that the 49ers investment will be used to generate transfer funds to strengthen the squad this summer.