The unidentified man had been placed on the nation's "Do Not Board" list the day before, but officials did not discover he was on the plane until after it took off.
The TSA is blaming the Centers for Disease Control for not giving them the information in time. The CDC is not commenting.
The man is now being treated in a San Bruno hospital. U.S. Airways is notifying other passengers on the flight, but health officials say the risk of the infection spreading is low because it was a relatively short flight of less than six hours.