In the state's murder and manslaughter case against Zarate, his defense lawyers said he found the weapon and it accidently discharged, shooting Steinle as he held it.
San Francisco's district attorney is defending the handling of a murder trial that ended with the acquittal of a Mexican man whose arrest set off a fierce national debate on immigration.
Each of the the two new federal charges carries a maximum of 10 years in prison if Jose Ines Garcia Zarate is convicted, the government said.
"When jurisdictions choose to return criminal aliens to the streets rather than turning them over to federal immigration authorities, they put the public's safety at risk", said U.S. Attorney General Jeff Sessions last week after the verdict in Garcia Zarate's local case was announced.
Defense attorneys for Garcia Zarate argued the gun, which had been stolen from the vehicle of a Bureau of Land Management ranger, was accidentally fired by Garcia Zarate.
District Attorney George Gascon said Tuesday that he still believes Jose Ines Garcia Zarate should have been convicted of murder in the 2015 death of Kate Steinle. Garcia Zarate is to be sentenced in state court December 14. He said it fired accidentally when he picked it up.
The Justice Department indictment makes no mention of the state's murder or manslaughter charges of which Zarate was acquitted.
That case drew national attention after then-candidate Donald Trump raised it as a justification for his proposed crackdown on illegal immigration and sanctuary cities.
Trump in a tweet called the not guilty verdict in the case "disgraceful" and said "No wonder the people of our Country are so angry with Illegal Immigration".
San Francisco prohibits city law enforcement officers from asking about immigration status or detaining people exclusively on the basis of civil immigration detainers after they are eligible for release.
Sanctuary City policies, which have been in place in San Francisco in some form since the 1980s and are used by several hundred other cities and counties nationwide, are meant to promote public safety by encouraging immigrants to report crimes and cooperate with police.
President Trump has threatened to withhold federal funding from cities with similar policies.