The search for Major League Baseball’s next commissioner has been unusual for an organization that has $8 billion in annual revenue and regards itself as a Fortune 500-caliber company. A search firm has not been hired, and there has been no attempt to vet a wide-ranging list of internal or external candidates.

Instead, Bud Selig, who has run the sport with a firm grip for 20 years and plans to step down in January at 80, has orchestrated his succession plan with secret meetings that, several owners said, have left little doubt about his wishes. Mr. Selig, they believe, would like the sport’s 30 owners to anoint his deputy, Rob Manfred, as baseball’s next commissioner.

But as Mr. Selig’s final season unfolds, Mr. Manfred’s candidacy is meeting turbulence from an unexpected antagonist: Jerry Reinsdorf, the 78-year-old owner of the Chicago White Sox and long one of Mr. Selig’s most loyal allies in the game. Mr. Reinsdorf has broken ranks and tried to upend the plan to slide Mr. Manfred into the commissioner’s office on Park Avenue, several owners say.

In discussions with other owners, Mr. Reinsdorf has raised questions about Mr. Selig’s transparency as commissioner and argued that Mr. Selig should play only an advisory role in picking his successor. Mr. Reinsdorf argued that, unlike owners who have hundreds of millions of dollars invested in their teams, Mr. Selig has no ownership in the game after he retires.