Eyewitness News has learned the deputy and suspect were taken to Duke Hospital.
Durham police said the deputy was shot in the foot, but did not say where the suspect was injured. Both are expected to be okay.
The suspect will be taken into police custody once he is released from the hospital. Two other suspects are currently under arrest in the case.
Officials said the confrontation centered around a narcotics investigation. At the scene, a white undercover police car had a bullet hole in the front window.
Authorities searched the restaurant's dumpsters in relation to the case and interviewed witnesses.
Further information about the incident is not available at this time.
Managers at Cracker Barrel said business went on as usual at the restaurant, but they would not comment on what went on inside the restaurant during the incident.