In a last-minute reversal, the State Department of Revenue revoked Wednesday a directive that would have taxed online retailers starting July 1.

Instead of enforcing that order — which faced a court challenge — Governor Charlie Baker’s administration will seek to implement the tax through a regulation this fall, according to his revenue department.

The Baker administration’s April directive aimed to collect sales taxes on out-of-state companies that sell more than $500,000 of merchandise in Massachusetts each year. Retailers subject to the order, also known as the “cookie tax,’’ would’ve included online companies that put digital cookies on the computers and phones of Massachusetts residents.

Brick-and-mortar stores in the state cheered the plan, arguing that sales tax exemptions for online retailers gives those companies an unfair advantage over local businesses.

But NetChoice Corp. and the American Catalog Mailers Associationchallenged the order in a lawsuit earlier this month, arguing it violated a federal law preventing taxes that discriminate against e-commerce.

After consulting with the state attorney general’s office, the Department of Revenue decided to pursue a regulation in lieu of enforcing the original directive next month, a Baker aide said. While the objective of the regulation would be the same, the difference is that the regulatory process requires public hearings and consultation with stakeholders.

For the Retailers Association of Massachusetts, which has pushed for a sales tax on online sellers for years, the department’s decision to opt for a regulation creates a delay but does not change the group’s support for such a tax — or the ultimate outcome, said Bill Rennie, the association’s vice president.

“The issue of sales tax parity between brick and mortar and online sellers, it’s been the No. 1 issue facing our members for a long time,’’ Rennie said. “We’ve waited decades for this problem to be addressed, and retailers locally want a level playing field with online sellers. And hopefully this regulation that the state intends to pursue will deliver that level playing field for us.’’

Steve DelBianco, executive director of NetChoice, wrote in an e-mail that he is pleased the state revoked the directive, which his organization argued against in court Wednesday.

“We’re very pleased with the result. After hearing our arguments in court yesterday, the [Department of Revenue] must have realized they were in for a prolonged and ultimately losing legal battle,’’ he said.

He pledged to challenge any regulation that advances the same aim.

The regulatory process might be completed by the fall.

Claire Parker can be reached at claire.parker@globe.com. Reach her on Twitter @ClaireParkerDC.