The two men were arrested after an employee called the police to report them for trespassing, though other customers in the shop told police they had been waiting inside the location to meet with a friend.
Video of Thursday's incident showed other patrons telling officers the pair were doing nothing wrong and appeared to have been targeted merely due to their race.
Both men were later released "because of lack of evidence" that they had committed a crime.
"Starbucks stands firmly against discrimination or racial profiling", he said.
He added that Starbucks would conduct training to prevent unconscious bias.
Abdul-Aliy Muhammad, one of the protest's organizers and co-founder of the Black and Brown Workers Collective, told The Associated Press: "We don't want this Starbucks to make any money today".
On Saturday, Philadelphia mayor Jim Kenney said he was "heartbroken" over the video and says Starbucks "should be a place where everyone is treated the same, no matter the color of their skin". Employees at the Philadelphia Starbucks had guidelines outlining scenarios where calling the police would be appropriate, such as threats and disturbances in the store, Johnson said.
The problems started when the men asked for the code needed to use the bathroom and were told it was only available for paying customers. "We really appreciate the transparency in the spirit with which we are working together", said Johnson. "Our store manager never intended for these men to be arrested and this should never have escalated as it did", Johnson said. The men, who were apparently meeting an acquaintance and had yet to order, were held in custody for eight hours. He later said the department would review its policies in dealing with such a situation in the future. They were released around 2 a.m. the following morning after the district attorney rejected the charges.