Officers arrested 19-year-old Frederick Lynn Palmer, of Partridge Street, and 20-year-old Michael D. Smith, of Danube Lane.
Both were charged with assault with a deadly weapon inflicting serious injury.
Palmer was also charged with injury to property.
Bonds for Smith and Palmer were set a $75,000.
The shooting happened shortly after 2:00 a.m. inside the parking deck near the intersection of Corcoran and Ramseur Streets.
The arresting officers were in the area when they saw shots being fired from a silver vehicle inside the parking deck.
One officer is with Durham police and the other is a Durham County sheriff's deputy, and both are assigned to the police department's new Violent Incident Response Team (VIRT).
The VIRT officers called for backup and officers were able to seal off the exits from the parking deck.
The Violent Incident Response Team (VIRT) is a recently formed unit comprised of eight Durham police officers and one Durham County sheriff's deputy.
The VIRT officers target violent crime, particularly gun crime, and violent offenders.