The "extraordinary circumstances" surrounding the death of 18-year-old Michael Brown and a request by Brown's family members prompted the order, Department of Justice spokesman Brian Fallon said in a statement.
"This independent examination will take place as soon as possible," Fallon said. "Even after it is complete, Justice Department officials still plan to take the state-performed autopsy into account in the course of their investigation."
The Justice Department already had deepened its civil rights investigation into the shooting. Officials said a day earlier that 40 FBI agents were going door-to-door gathering information in the Ferguson, Missouri, neighborhood where Brown, who was unarmed, was shot to death in the middle of the street on Aug. 9.
David Weinstein, a former federal prosecutor who supervised the criminal civil rights section of Miami's U.S. Attorney's office, said a federally conducted autopsy "more closely focused on entry point of projectiles, defensive wounds and bruises" might help that investigation, and that the move is "not that unusual."
He also said federal authorities want to calm any public fears that no action will be taken on the case.
President Barack Obama, who has been getting regular briefings on the situation in Ferguson while on vacation, also was to be briefed by Holder upon returning Monday to the White House.
The Justice Department's latest announcement followed the first night of a state-imposed curfew in Ferguson, which ended with tear gas and seven arrests after police dressed in riot gear used armored vehicles to disperse defiant protesters.
Missouri State Highway Patrol Capt. Ron Johnson said protesters weren't the reason for the escalated police reaction early Sunday after the midnight curfew took effect, but a report of people who had broken into a barbecue restaurant and taken to the roof, and a man who flashed a handgun in the street as armored vehicles approached the crowd of protesters.
Also overnight, a man was shot and critically wounded in the same area, but not by police; authorities were searching for the shooter. Someone also shot at a police car, officials said.
The protests have been going on since Brown's death heightened racial tensions between the predominantly black community and mostly white Ferguson Police Department, leading to several run-ins between police and protesters and prompting Missouri's governor to put the Highway Patrol in charge of security.
Ferguson Police waited six days to publicly reveal the name of the officer and documents alleging Brown robbed a convenience store before he was killed, though Chief Thomas Jackson said the officer did not know Brown was a suspect when he encountered him walking in the street with a friend.
Gov. Jay Nixon, who imposed the curfew after declaring a state of emergency as protests turned violent to start the weekend, said Sunday morning on ABC's "This Week" that he was not aware the police were going to release surveillance video from the store where Brown is alleged to have stolen a $49 box of cigars.
"It's appeared to cast aspersions on a young man that was gunned down in the street. It made emotions raw," Nixon said.
Police have said little about the encounter between Brown and the officer other than that a scuffle ensued after the initial stop, the officer was injured and Brown was shot. Witnesses say the teenager had his hands in the air as the officer fired multiple rounds.
"When you're exhausted, when you're out of resources, when you're out of ammunition, you surrender," Brown's uncle, pastor Charles Ewing, told worshippers during a Sunday sermon at Jennings Mason Temple in Ferguson. "He surrendered, and yet he died."
In announcing the standing curfew in Ferguson, Nixon said many protesters were making themselves heard peacefully but the state would not allow looters to endanger the community. Johnson, the Highway Patrol captain, had said police would not enforce the curfew with armored trucks and tear gas and would communicate with protesters and give them ample opportunity to leave. Local officers faced strong criticism earlier in the week for their use of tear gas and rubber bullets against protesters.
As the curfew deadline arrived early Sunday, most protesters left the streets, but those who remained protesters refused to leave the area as officers spoke through a loudspeaker: "You are in violation of a state-imposed curfew. You must disperse immediately."
As officers put on gas masks, a chant from the distant crowd emerged: "We have the right to assemble peacefully."
A moment later, police began firing canisters into the crowd. Highway Patrol Spokesman Lt. John Hotz initially said police only used smoke, but later told The Associated Press they also used tear gas canisters.
Jackson, the Ferguson police chief, has identified the officer who shot Brown as Darren Wilson, a six-year police veteran who had no previous complaints against him. Wilson has been on paid administrative leave since the shooting and the department has refused to say anything about his whereabouts. Associated Press reporters have been unable to contact him at any addresses or phone numbers listed under that name in the St. Louis area.