The vehicles were attached by the agency under the Prevention of Money Laundering Act (PMLA) in the past.
The Enforcement Directorate (ED) had in March obtained the permission of a special PMLA court in Mumbai for auctioning 13 cars of the Modi-Choksi duo as part of its money laundering probe in the $2 billion alleged bank loan fraud.
The e-auction was carried out by Metal Scrap Trade Corporation (MSTC) Ltd, it said in a statement.
The Income Tax Department had last month auctioned several art works that were owned by absconding diamond merchant Nirav Modi for Rs 59.37 crore.
The ED and the CBI are investigating Nirav Modi, his uncle Choksi and others for alleged money laundering and corruption to perpetrate the alleged scam in the Brady House branch of the PNB in Mumbai that was unearthed last year.
While Nirav Modi has been arrested in London recently and India is seeking his extradition, Choksi is said to be in the Caribbean nation of Antigua and a similar legal action against him is on too.