The star and his crew on the BBC show had to abandon their cars at the roadside as they were pelted with stones.
Trouble erupted after it emerged the team were using a Porsche with the registration number H982 FKL, which some people suggested could refer to the Falklands conflict of 1982.
This is my car on its last day in Argentina. Note the plates that everyone says caused offence. pic.twitter.com/mCfncbMa6F
— Jeremy Clarkson (@JeremyClarkson) October 4, 2014Clarkson told The Sun the mob shouted "burn their cars" and tried to attack them with pickaxe handles.
He said: "I've been to Iraq and Afghanistan, but this was the most terrifying thing I've ever been involved in.
"There were hundreds of them. They were hurling rocks and bricks at our cars.
"This is not just some kind of jolly Top Gear jape - this was deadly serious."
In a series of tweets, Clarkson said someone could have been killed during the incident after returning to the UK this morning.
All TG crew now safely out of Argentina. I just got back to UK. Horrified to see so many newspapers have the story completely wrong.
— Jeremy Clarkson (@JeremyClarkson) October 4, 2014The number plate WAS a coincidence. When it was pointed out to us, we changed it. As pics in this morning's Mail show.
— Jeremy Clarkson (@JeremyClarkson) October 4, 2014And these war veterans we upset. Mostly they were in their 20s. Do the maths.
— Jeremy Clarkson (@JeremyClarkson) October 4, 2014They threw us out for the political capital. Thousands chased crew to border. Someone could have been killed.
— Jeremy Clarkson (@JeremyClarkson) October 4, 2014This was not a jolly jape that went awry. For once, we did nothing wrong.
— Jeremy Clarkson (@JeremyClarkson) October 4, 2014We had planned a good ending for the show. But thanks to the government's foolishness, it's now even better.
— Jeremy Clarkson (@JeremyClarkson) October 4, 2014My profound thanks to all the people who helped. And to the sensible Argentinians who have apologised.
— Jeremy Clarkson (@JeremyClarkson) October 4, 2014BBC bosses have said the number plate was merely a coincidence and was not chosen deliberately, but it led to protests in Argentina, including a demonstration by a group of war veterans outside the hotel used by the show team.
A story about their visit in the Patagonian daily newspaper Diario Jornada is headlined: "Top Gear is filming in Patagonia and there's controversy."
The paper says: "Even though the BBC authorities asked the popular presenter Jeremy Clarkson to behave himself during his time in Argentina, he chose to use the provocative number plate H982 FKL on his Porsche, in reference to 1982 Falklands (Malvinas)."
But Clarkson has insisted: "We knew absolutely nothing about the number plate, it was just an unbelievable coincidence."
The executive producer of Top Gear, Andy Wilman, back the controversial presenter's argument.
"Top Gear production purchased three cars for a forthcoming programme; to suggest that this car was either chosen for its number plate, or that an alternative number plate was substituted for the original, is completely untrue," he said.
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A BBC spokesman said: "We're pleased the team is safe and would like to thank all of those who have helped. As the executive producer has made clear, the number plate issue is a very unfortunate coincidence."
The team from the BBC2 show were in South America filming a special on a remote highway passing through Chile and Argentina.
The programme has already run into problems this year, with one edition found to be in breach of Ofcom's broadcasting code for the use of a racially offensive term during a two-part special filmed in Burma, following a complaint from a viewer.
And Clarkson also had to apologise after unbroadcast footage emerged in which he appeared to use the n-word, although he denied actually saying it.