Marco Proano, 41, is accused of using unreasonable force against two teenagers who were injured.
The video shows Proano shooting multiple times at the vehicle as the driver tries to back away. The car then hits a streetlight before one injured teen stumbles out.
Police had pulled over the car with six teens for speeding, according to CNN affiliate WLS
. One teen was wounded in the shoulder, the other in his hip and heel.
The victims suffered bodily injuries because of "unreasonable force by a police officer," according to the indictment.
"When a police officer uses unreasonable force, it has a harmful effect on not only the victims, but also the public, who lose faith and confidence in law enforcement," said Zachary T. Fardon, US Attorney for the Northern District of Illinois.
He said his office will continue to "vigorously" pursue civil right prosecutions of police officers to "strengthen trust in the police."
The Chicago police department said it is fully cooperating with the US attorney's office and has "zero tolerance for proven misconduct."
Proano was discharged from the police force last year during the course the investigation, officials said.
The injured teenagers settled a lawsuit against the city of Chicago for $360,000, according to CNN Affiliate WBBM.
One of the teens was charged with possession of a stolen vehicle but the judge in the case found prosecutors couldn't prove he knew the car was stolen, WBBM reported
Proano's attorney, Dan Herbert, said he will talk about the indictment at his client's arraignment next Thursday at the federal courthouse in Chicago.