Naidoo told the state capture inquiry that the E-Class Mercedes was specifically purchased for Mthethwa, who is currently the sports, arts and culture minister.
Naidoo, who is now in witness protection, said he personally delivered the car to Mthethwa's Pretoria residence.
Naidoo said the car was purchased for about R373,000 using funds from the secret service account.
The commission has previously heard how the account was looted by senior Crime Intelligence officials, including the division's former boss Richard Mdluli, to purchase luxury vehicles, bribe journalists and pay for overseas flights and accommodation.