He and co-hosts Richard Hammond and James May fled their hotel and headed for the airport when the lobby was invaded by angry war veterans.
The remaining camera men, sound recordists, fixers and producers were pelted by stones as they were forced to escape to Chile overland, abandoning the offending Porsche at the border.
The controversy was only fuelled when police found another set of plates reading BE11 END in the vehicle.
A spokeswoman for the BBC TWO show originally said that a member of the Top Gear team had spotted the advert for the Porsche online and sent a member of the production team to buy it in August- just a month before filming for the South American Christmas Special began in Argentina.
She subsequently admitted that they had received a copy of the vehicle's registration document before buying it but claimed it "would not have been read in any minute detail" and that it was still bought "blind".
"Top Gear buys a huge number of cars," she said. "They just sign, they don't read it in any great detail."
Meanwhile, the classic car dealer who sold the Porsche to the BBC revealed that he had hoped it would be used on a long-running series like Inspector Morse.
Mark Waring, of Surrey-based Rennsport Classics, said he had no idea that the car was to be used by Jeremy Clarkson on Top Gear.
"These rare cars are cherished, so when the BBC rang and explained they wanted to buy it, I had hopes that it would features on a series like Morse and be on screen for many years," he said.
"It is the type of car that would be used on Morse. It's a manual tourer, they are very rare. Naturally, this is not the kind of publicity that I had anticipated.
"I did ask what it would be used for but was told they could not and would not tell me."
Mr Waring said the unnamed BBC employee who purchased the car in August was specifically looking for a manual 928 and would not have had much choice in the market place.
He said that after the Top Gear debacle became public knowledge, he contacted the person from whom he had bought the Porsche as a matter of courtesy.
"If people approach me to sell a cherished car, I endeavour to sell it to someone who will continue to look after it in a way the previous owner had," he said.
"I explained what I had done and how the transaction had been conducted. I explained that although I knew the BBC were buying the car, I was not aware it was Top Gear that it was going to be used on.
"He understood that if you find out two days later that the car has been fired into space, there is nothing you can do about it. You can only try your best. As passionate as I am about them, they are only cars."
He said he would never disclose the personal details of either the buyer or a seller of any car due to client confidentiality.
The car is now expected to be scrapped or sold at auction. And in a further blow for Clarkson and his team, Argentina is considering whether to open a formal inquiry as the use of different number plates to those that appear in the car's official documentation is a crime which carries a maximum three year prison sentence.
