Zarate, who was arrested shortly after the shooting in 2015, was credited for time served.
The San Francisco Sheriff's Department handed Jose Ines Garcia Zarate over to U.S. Marshals on warrants stemming from federal gun charges.
An illegal immigrant acquitted in a fatal San Francisco shooting, in a verdict condemned by President Donald Trump, was sentenced to three years in prison on a lesser gun charge on Friday.
The 45-year-old Mexican national, Jose Ines Garcia Zarate, has been held behind bars since his arrest in the July 2015 shooting death of Kate Steinle, and was fully credited for the three-year sentence, a spokesman for the San Francisco district attorney's office said.
The San Francisco Sheriff's Department handed Garcia Zarate over to U.S. Marshals on Friday on warrants stemming from federal gun charge related to the Steinle incident, sheriff's department spokeswoman Nancy Crowley said.
A San Francisco Superior Court jury had found Garcia Zarate not guilty of murder and manslaughter charges in connection with Steinle's death. Jurors found him guilty of being a felon in possession of a firearm.
Garcia Zarate had found the gun that killed Steinle. It accidentally discharged, with the bullet ricocheting off the ground at a crowded pier before striking the 32-year-old woman, his defense attorneys have said.
Prosecutors claimed Garcia Zarate intentionally fired the gun, but they said they accepted the jury's verdict.
Trump, who used the Steinle case as a rallying cry against the policies of so-called sanctuary cities for immigrants during his successful run for the presidency, has called the jury's verdict "disgraceful."
Just days after he was acquitted in San Francisco, Garcia Zarate was indicted on federal charges of being a felon in possession of a firearm and being an illegal immigrant in possession of a firearm.
The latest criminal counts against Zarate would not violate the constitutional protection against double jeopardy, which prohibits being tried twice on the same charges, because they differed legally from the state court charges, a U.S. Department of Justice spokesman said last month.
A representative for the Office of the Federal Public Defender could not immediately be reached for comment.
Garcia Zarate faces a maximum sentence of 10 years in prison on each charge if convicted.
Immigration agents have vowed to eventually deport Garcia Zarate, who first came to the United States as a juvenile and was deported multiple times.