The plates had been discarded when the limousine was sent for upgrades after President Kennedy was shot dead in Dallas, Texas in November 22, 1963.
The company's owner retrieved them and passed them on to his daughter.
The plates, bearing number GG-300, had been expected to raise close to USD 40,000 at the auction in Dallas.
"I was aware of their significance," said Jane Walker, who inherited the plates and kept them in a kitchen drawer.
The auction company said the plates were bought by a "high-end Kennedy collector" who wanted to remain anonymous, the BBC reported.
Kennedy, 46, was fatally shot while traveling with his wife Jacqueline, Texas Governor John Connally, and Connally's wife Nellie, in a presidential motorcade.