Police said the incident began just after 3 a.m. when officers responded to a 911 call for a robbery at Broad and Fitzwater streets.
A couple had reported to police that they were robbed of a purse, a cell phone and a wallet by three men at gunpoint.
Shortly after an officer spotted one of the suspects on South Street and a chase ensued, authorities said.
According to investigators one of the suspects was found hiding in an abandoned home on the 1300 block of Kater Street.
Police said the man had a loaded gun in his hand and pointed it at the officer.
"He did point the gun at the officer in very close, close, close quarters, so there's no mistaking it was an officer. The officer was not only operating a marked police vehicle but it's a third district officer in full uniform," said Philadelphia Police Chief Inspector Scott Small. "The suspect had no doubt that he was pointing a gun at a uniformed police officer."
The officer fired two shots but did not hit the suspect.
"At this time this appears to be a justifiable police discharge," said Small.
Authorities said a fight ensued and the officer injured his knee and hand but was able to get the gun from the suspect and the suspect was taken into custody.
Police said a second suspect fitting the description given was located at 11th and Washington streets and taken into custody.
Police are still searching for the third suspect. They say he is believed to be wearing dark clothing and might have gotten away on a bike.
According to police, no one was seriously hurt during the incident, however, some neighbors said they are upset about this armed robbery.
"To be honest we have two small kids, we have a 3-year-old and an 8-year-old, so the last thing you want to hear about in pretty much your street is that somebody got robbed at gunpoint," said Eric Balchunas, of South Philadelphia.