Johnson told a news conference it was against departmental policy to fire at or into a moving car when the vehicle was the only potential use of force by a suspect, and police were taking a hard look at training and tactics following the shooting.
Authorities on Friday released videos that captured the moments before and after police shot Paul O'Neal, 18, on July 28, but not the shooting itself because a police officer's body camera was not recording. No firearms were found on O'Neal, who was shot in the back, according to police.
Johnson was named in March to lead the department, which is facing accusations of racism and a federal investigation into its practices after the city waited more than a year to release video of a separate 2014 fatal shooting by officers.
On Saturday, he said the ongoing investigation prevented him from discussing details about the O'Neal shooting.
"I was concerned by some of the things that I saw on the videos and that is why we took such a swift action that we did last week to relieve the three officers of their police powers," Johnson said.
The video footage released on Friday shows two officers firing at a stolen car driven by O'Neal after it sped past them, the car crashing into a police car, and O'Neal running into a backyard where he was shot. It does not show the shooting.
Johnson said the lack of a body-camera video of the O'Neal shooting is under investigation, though he noted that the officers in that police district had the cameras for only about a week before the shooting.
Civil rights activist Reverend Jesse Jackson said the lack of a complete video accounting of O'Neal's shooting showed a cover-up and a lawyer for O'Neal's family called for a special prosecutor to investigate the killing.
The union representing Chicago police officers urged the public not to rush to judgment.
Dozens of protesters demanding swift action against the officers involved in O'Neal's shooting demonstrated outside Chicago police headquarters on Friday night.
A string of high-profile killings of black men by police in various U.S. cities in the past two years has renewed a national debate about racial discrimination in the criminal justice system and given rise to the Black Lives Matter movement.