It happened around 11:20 p.m. at the Philly Stop Shop, which is located on the 2900 block of North 5th Street.
When officers responded, they spotted the three suspects leaving the business.
Police followed one suspect who ran away, while two others ran back inside the business.
The investigation quickly turned into a barricade situation until SWAT cleared the property around 2 a.m. with no one in custody.
Police believe the suspects were able to escape through a window on the second floor.
During the incident, police say the 47-year-old store owner was pistol-whipped and taken to the hospital in stable condition. A 37-year-old woman who was inside at the time of the robbery was also injured.
Monique Varona says her family has been in business on the block for nearly five decades and witnessed its decline.
"Everybody was very united and everybody got along. There was not that much robbing and stealing. Hopefully, things will change after this for the better," said Varona.
"You have to be careful. I just gotta watch my back," she added.
Officers were able to recover a suspect's gun and the vehicle they were driving. Police also found zip ties and other items inside the car that officers believed were going to be used to commit the crime.
Anyone with information on the suspects is asked to call police at 215-686-TIPS.