The cover, often reserved for rock stars and top celebrities, features the 19-year-old teen suspect in a photo taken from one of Tsarnaev's social media accounts.
In the cover photo, Tsarnaev is sporting shaggy hair and staring intently into the camera. The headline on the cover reads, "The Bomber. How a popular, promising student was failed by his family, fell into radical Islam and became a monster."
CVS, Walgreens and Rite Aid announced via Twitter that they would pull the issue from their shelves.
The cover backlash exploded on social media, causing Rolling Stone to trend on Twitter for seven hours straight in the United States.
ABC News' Aaron Katersky contributed to this report.