"Hatred and violence on the basis of religion can have no place in our society," US Attorney General Jeff Sessions said in a press release, announcing the charges against Bowers, 46, of Baldwin, state of Pennsylvania, Xinhua news agency reported.
According to the indictment, Bowers drove to the Tree of Life Synagogue in Pittsburgh's Squirrel Hill neighbourhood last Saturday where members of three congregations gathered to engage in religious worship.
The indictment alleges that after entering the building, Bowers, armed with multiple firearms, opened fire, killing and injuring worshippers, as well as injuring multiple responding public safety officers.
Inside the building, Bowers made statements indicating his desire to "kill Jews."
The victims include 11 worshipers at the synagogue who were killed, and two members of the congregations who were critically injured by Bowers. Nine other members of the congregations escaped unharmed.
In addition, four law enforcement officers were injured while trying to stop Bowers' rampage.
"Today begins the process of seeking justice for the victims of these hateful acts, and healing for the victims' families, the Jewish community, and our city," US Attorney Scott Brady said.
"Our office will spare no resource, and will work with professionalism, integrity and diligence, in a way that honors the memories of the victims," Brady said.
The funerals for the victims began on Tuesday and are continuing through the rest of the week.
US President Donald Trump and first lady Melania Trump travelled to Pittsburgh on Tuesday afternoon to offer condolences to the victims of the Synagogue shooting.
The FBI conducted the investigation, leading to the indictment in this case.
Bowers, a truck driver, remained jailed without bail ahead of a preliminary hearing scheduled for Thursday.
He faces a maximum possible penalty of death, or life without parole, followed by a consecutive sentence of 535 years of imprisonment.
An indictment is a formal accusation of conduct, not evidence of guilt. A defendant is presumed innocent unless and until proven guilty.