The arrest of the 21-year-old was captured by the dashboard-mounted camera of a patrol car in Shelby, North Carolina.
The clip shows armed officers approaching the alleged gunman's car on a busy street, before frisking and handcuffing him without incident.
After pulling Roof over, two officers approach the black Hyundai Sedan with weapons drawn, but one holsters his weapon as he nears the driver's side window.
More police arrive on the scene as Roof exits the vehicle and is placed in handcuffs while facing his vehicle.
Officers are seen congratulating each other with high fives as the huge manhunt ends 16 hours after the shooting.
The clip was released as major retailers, including eBay and Amazon, halted sales of the Confederate flag embraced by Roof.
The suspect was arrested at around 10:44am last Thursday after a female motorist spotted his car.
Debbie Dills, a florist and minister, was running late for work when she recognised the vehicle at a red light.
Roof is charged with nine counts of murder and one weapons charge.
The police chief who arrested Roof has said officers bought the suspect a Burger King meal after detaining him as he complained of hunger.
Chief Jeff Ledford told the Charlotte Observer that when pulled over, the accused lowered his window and handed over his driver's licence to officers, saying: "I'm Dylann Roof."
Authorities have said they found a .45-calibre handgun in the car.
Roof reportedly told officers he had been heading to Nashville, Tennessee, because he had never been there before.