A witness can be heard on the video calling the arrest "ridiculous."
The video has been viewed more than 3 million times.
Starbucks released a statement Saturday, apologizing for the incident.
Starbucks' CEO Kevin Johnson told The Associated Press that he wanted to apologize personally to the two men.
Johnson called the situation "disheartening" and that it led to a "reprehensible" outcome, the AP reported.
Police are conducting an internal investigation. On Saturday, Philadelphia Police Commissioner Richard Ross told The Associated Press his officers did nothing wrong. Ross claims Starbucks employees called police to say two men were trespassing, after the men's request to use the bathroom was denied because they had not made a purchase. Ross said that the men were asked three times to leave and refused, at which point they were arrested.
The Associated Press contributed to this report.