Facebook Inc. pulled its data-security app from Apple Inc.’s app store after the iPhone maker ruled that the service violated its data-collection policies, according to a person familiar with the matter.

Apple’s decision widens the schism between the two tech giants over privacy and is a blow to Facebook, which has used data gathered through the app to track rivals and scope out new product categories, The Wall Street Journal reported last year. The app, called Onavo Protect, has been available as a free download through...