The case, Apple v. Pepper, alleges that Apple is raising prices for consumers with its mandatory 30% cut of any app sales consumers make. This commission structure results in higher prices for consumers, the plaintiffs argued.
With Monday's ruling, it will kick the case back to a lower court, where iPhone owners and Apple will continue what is likely to be a lengthy legal battle.
Apple said that it was an agent for app developers and that it neither owned nor sold the apps itself. Based on its own interpretation of the legal precedent, Apple argues that consumers can only sue the developers due to their role setting prices.
"Apple's line-drawing does not make a lot of sense, other than as a way to gerrymander Apple out of this and similar lawsuits", Justice Brett Kavanaugh wrote in a 14-page opinion.
This meant, for example, a consumer could sue a retailer, but not a wholesaler or a manufacturer of a product. Justice Neil Gorsuch filed the dissenting opinion, joined by Chief Justice John Roberts and Justices Clarence Thomas and Samuel Alito.
Apple did not immediately respond to a request for comment on the ruling.
Last year, iOS 12 gave a stay of execution to older devices by supporting exactly the same iGadgets as iOS 11. For subscriptions, Apple collects a 15 percent share after the first year.
"The plaintiffs seek to hold retailers to account if the retailers engage in unlawful anticompetitive conduct that harms consumers who purchase from those retailers", Kavanaugh wrote.
French website iPhoneSoft claims the models being targeted by Apple's change of mind are iPhone 5s, iPhone SE, iPhone 6, and iPhone 6 Plus. Should Apple lose the case it might be forced not just to allow third-party app stores, but to pay up to triple in damages as a deterrent.
It's worth noting that the Supreme Court did not rule Apple a monopoly, but rather allowed the suit to proceed.