Secretary of State Kim Guadagno decided Tuesday that Lewis can't continue his run for state Senate as a Democrat.
She ordered the 49-year-old's name to be stricken from the June primary ballot.
The decision by Guadagno, a Republican, can be appealed.
Guadagno rejected an administrative law judge's recommendation that Lewis be allowed to stay in the race to represent the state's south-central region.
Republicans challenged Lewis' run, saying he voted in California until recently.
The former track star told The Philadelphia Inquirer Gov. Chris Christie tried to talk him out of running.
The Christie administration says Lewis misunderstood the talk.