According to police, Babbitt was arrested on Saturday after an officer in Fairfax, Va., observed his car driving on the wrong side of the road.
Babbitt was taken into custody and later released on a personal recognizance bond.
Babbitt was the only person in the vehicle, and he was cooperative at the time of his arrest, police said.
The Department of Transportation, which includes the FAA, says the leave was taken at Babbitt's request. Deputy Administrator Michael Huerta will serve as acting administrator.