The review follows pressure from civil rights groups to investigate the death of Mario Woods at the hands of police.
His shooting in a hail of bullets in December sparked widespread outrage.
The force is the latest in the US to face attention over fatalities involving African-Americans.
However the review will only provide recommendations, not court-enforceable reforms.
"We will examine the San Francisco Police Department's current operational policies, training practices and accountability systems, and help identify key areas for improvement," US Attorney General Loretta Lynch said in a statement.
When the review is completed the Justice Department will give San Francisco police a list of procedures it can follow to insure more fairness in its dealings with citizens.
Local residents and citizen groups had been calling for the federal government to examine video footage of San Francisco police gunning down Woods, who was suspected of carrying a knife.
Videos of his death under intensive fire went viral in December.
San Francisco Mayor Edwin Lee wrote to Ms Lynch asking her to launch an investigation in the interests of openness and maintaining good relations between police and the city's population.
Police in cities throughout the US have been subjected to intense scrutiny for using excessive and lethal force against suspects, many of them black.
Other American police departments such as Baltimore have asked the Justice Department to conduct similar inquiries following allegations of discrimination.
In Baltimore's case a review of police practice was already under way when black detainee Freddie Gray was killed in April.
Gray's death quickly became a flashpoint in a national debate over police use of force - especially against black men.
Protests raged for several days and at one point turned violent, forcing officials to declare a state of emergency and to deploy national guard troops across the city of 620,000 people.
The US Justice Department has announced an investigation into the San Francisco police force, eight weeks after the fatal shooting of a 26-year-old black man provoked fury in the city.