Scott Forstall, senior vice president for iPhone and iPad software, and John Browett, senior vice president of retail operations, will both leave the company, Apple said in a release. Their responsibilities will be distributed among other managers.
Apple said the changes were intended to "encourage even more collaboration" between its hardware, software and services teams. Tensions between Forstall and other senior executives had been building for some time, the New York Times reported at its website.
The retail team, which runs the company's Apple stores, will report to chief executive Tim Cook until a replacement can be found for Browett, who joined the company earlier this year.
Apple didn't say why Browett and Forestall were leaving, but both have presided over missteps this year.
Browett cut staffing hours at Apple's retail stores, a move the company reversed and acknowledged as a mistake.
Forstall's division launched a software update in September that replaced Google Maps with Apple's first mapping application. It quickly drew unfavorable comparisons to the software it was replacing, and Apple apologized.
While Browett's departure is immediate, Forstall will remain as an adviser to Cook until he leaves, Apple said. His responsibilities will be divided among other Apple veterans such as Jony Ive, Eddy Cue, and Craig Federighi.
Forstall joined Apple in 1997 with the company's purchase of Steve Jobs' NeXT startup. Apple credits him as one of the original architects of Mac OS X.
Federighi, who is now in charge of the Mac OS, will add iOS development to his responsibilities, Apple said.
Ive, who often appears in Apple advertising and is the chief designer behind the distinctive look of Apple hardware, will take responsibility for the look and feel of Apple's software.
And Cue, head of Apple's online services and iTunes, will assume responsibility for Maps and Siri, the "virtual assistant" application on the iPhone and iPad.
Apple stores sell more per square foot than any other chain in the U.S., yet they account for just 12 per cent of Apple's overall sales. They're positioned as ambassadors for Apple's brand and products, and provide customers with an easy way to access in-person technical support.