The incident happened around 7:30 p.m. near 17th and Cumberland streets.
Police Commissioner Kevin Bethel said both suspects had exited the vehicle and were being searched when an armed suspect's gun discharged, striking the officer in the leg.
The officer was taken to Temple University Hospital, where he was listed in stable condition.
"We're fortunate he received a gunshot wound to his leg, but he's doing extremely well," said Bethel.
Officials provide update after officer shot in leg in North Philly
Bethel said the injured officer and his partner were in the area responding to reports of gunfire prior to the traffic stop.
"We had some gunshots and gun activity up in that area. As a normal process, we send our special team in there, highway patrol, to settle things down," stated Bethel.
At least one person was taken into custody. Officials did not immediately release information about potential charges.
Police said the injured officer has been with the department for 20 years.
No other injuries were reported.
Further details on how the shooting occurred remain under investigation.