SAN JOSE — San Jose’s antitrust case against Major League Baseball over the long-stalled plan to move the Oakland A’s to the South Bay is now headed to a federal appeals court — but delay on a final outcome will continue to be the name of the game.

San Jose can immediately appeal an earlier order dismissing the city’s key federal antitrust arguments, U.S. District Judge Ronald Whyte indicated, a move that elevates the legal stakes in a case that challenges MLB’s cherished antitrust exemption. Whyte plans a final decision later, but it came over the objections of MLB lawyers.

At the same time, Whyte intends to abandon his oversight of remaining legal claims made under state law, which argue that MLB has interfered with San Jose’s interests by refusing to act for four years on the A’s bid to move to Silicon Valley and the city’s option agreement with the team to buy land for a ballpark. The city will refile those claims in a new case in the state courts.

The developments sidetrack the effect of a recently disclosed letter from MLB Commissioner Bud Selig to A’s owner Lew Wolff in June, a day before the city’s lawsuit was filed, that apparently rejected the A’s move to San Jose. MLB lawyers last week revealed the secret letter in court papers, asserting that it undermines San Jose’s argument that it is being harmed because the league has refused to decide the issue.

At one point Friday, Whyte pressed MLB lawyer John Keker as to why the letter has not been made public or turned over to the city, also asking whether it was an “unequivocal” denial of the A’s plan. Keker replied: “What the A’s asked the commissioner to approve was unequivocably denied.”

It is unclear how far the letter went in denying the A’s pursuit of a San Jose home. Wolff, in an interview with this newspaper, has appeared unfazed by it, strongly reaffirming his intent to continue to push MLB to back the A’s quest to move to San Jose. The San Francisco Giants oppose the move, asserting their territorial rights to the South Bay; as a result, the A’s plan must be approved by a three-fourths majority of the league’s owners.

Keker declined to comment Friday on the latest developments. Joe Cotchett, San Jose’s lawyer, said it was a major win for the city to be allowed to appeal the antitrust arguments immediately to the 9th U.S. Circuit Court of Appeals, rather than wait until the rest of the case was decided.

“The court is going to be able to get to the bottom line,” he said.

Whyte earlier this year dismissed San Jose’s antitrust claims, which challenge MLB’s more than 90-year-old antitrust exemption and its grip on deciding whether teams can relocate. The issue is unlikely to be decided anytime soon, as it must go through the 9th Circuit and is expected to later reach the U.S. Supreme Court.

The A’s have envisioned building a privately financed ballpark on land near the Diridon rail station, not far from the city’s hockey arena, but the plan is rife with obstacles. Among other issues, it remains unclear whether the city has the right to sell the land to the A’s, and that is tied up in a separate legal challenge in the state courts. And there would have to be a public vote on the stadium if it ever gains MLB approval.

The A’s have been seeking that approval since 2009, hoping to move from Oakland’s O.Co. Coliseum, one of the most antiquated venues in the league. Oakland city leaders have been working on a plan to retain the A’s, as well as the Oakland Raiders, with a stadium complex on the same Coliseum site, but the A’s have yet to support the proposal.

Howard Mintz covers legal affairs. Contact him at 408-286-0236. Follow him at Twitter.com/hmintz.