It happened just after 6:00 a.m. Wednesday at an apartment complex in the 800 block of Riverside Drive.
Officer Francis Whalen was attempting to arrest 26-year-old Devon Guishard.
Police say that suspect opened fire, hitting Officer Whalen in the stomach but the officer returned fire, killing Guishard.
Investigators recovered Guishard's gun at the scene. They say the serial numbers were removed and it was loaded with 13 rounds.
Whalen was wearing a bullet proof vest and was taken to Aria Health/Torresdale with stable vital signs, and later released.
As with all police-involved shootings, he has been placed on administrative duty pending an internal investigation.
Whalen is a married father of two children, a 17-year veteran of the force, and assigned to SWAT.
In addition, this is the second time he has been shot in the line of duty. Back in December, 2010, Whalen was hit in the chest but was protected by his bullet proof vest.
Police Commissioner Charles Ramsey said that because the officer is part of SWAT, his vest has a special flap that protected him.
"If this had been a patrol officer we'd be having a different discussion," Ramsey said.
Thank you for the support of our officer who was shot in the line of duty this morning. He is currently recovering in stable condition— Philadelphia Police (@PhillyPolice) July 22, 2015
Guishard was wanted in the killing of 25-year-old Megan Doto.
Doto was shot and killed by a stray bullet on September 14th in the Frankford section of Philadelphia. She was eight months pregnant at the time.
Police said Guishard fired 11 shots down the 1400 block of Adams Street, targeting a white sedan that had circled the block.
The intended target was not hit, police said.
Doto was pronounced dead at Temple University Hospital.
Her baby was delivered by emergency C-section after her mother was mortally wounded, but the child died hours later.