Circuit Court judge Ted Coleman denied a state motion to dismiss a lawsuit brought by Sultaana Freeman, whose licence was revoked when she refused to replace her picture with one showing her face unveiled.
Mrs Freeman filed the suit in January, saying her constitutional right to religious freedom had been violated.
But the Florida state officials argued that her refusal to uncover her face jeopardised public safety.
'Hyper-sensitive'
Mrs Freeman, a US citizen who converted to Islam five years ago, wears a veil called a niqab which only leaves her eyes uncovered.
When she applied for a licence in Florida last year after moving from Illinois, she had no problems using a photograph with her face covered, said her attorney, Howard Marks.
It was only after the 11 September attacks that the Florida Department of Motor Vehicles told her to replace the picture, he said.
He claimed that Mrs Freeman's constitutional rights to freedom from religious persecution, to expression and for equal protection under the law were being violated.
But the Florida Department of Highway Safety and Motor Vehicles accused Mrs Freeman of being "hypersensitive", arguing that legitimate public safety concerns should over-ride her individual rights, particularly in the wake of the terror attacks last September.
Jason Vail, an assistant state attorney, said the requirement did not target religion. "It targets everyone," he said.
"The reasonable person in Florida is not offended by having to sit for a drivers' licence photo," he added.
Civil rights and privacy advocates with the American Civil Liberties Union (ACLU) have backed Mrs Freeman's lawsuit.