A viewer contacted the BBC to complain about a controversial segment of the BBC Two motoring show in which Clarkson discussed the new Prius campervan.
Describing the look of the vehicle, Clarkson simulated "really ugly" facial growths with his hands and then slurred his speech to mimic the title character (based on the real-life Joseph Merrick) from the movie The Elephant Man.
His Top Gear co-presenter Richard Hammond called it the "elephant car", and then Clarkson concluded: "You've got a double bed in the back and then another one in that growth. That is not a car that you could talk to at a party unless you were looking at something else, is it?"
The producers of the motoring programme responded to the complaint by saying that the "absurdity of the context" would have shown that Clarkson and Hammond did not mean to offend.
It was noted that Clarkson himself was the butt of the joke for much of the sequence, but the BBC also said that it was "genuinely sorry if the item had caused any upset".
However, the complaint was not satisfied with that response, as he wanted a public apology from Clarkson, and so escalated the matter to the BBC Trust.
In a ruling issued yesterday, the Trust upheld the complaint after disagreeing with the BBC's assertion that the comments were not justified by the editorial context.
The Trust's Editorial Complaints body particularly noted that the line, "That is not a car that you could talk to at a party unless you were looking at something else, is it?" played on a "stereotypically negative reaction" to facial disfigurement.
"The Committee agreed that this comment was not specifically referring to the character Joseph Merrick," said the Trust.
"Taken together with the references at the beginning of the exchange, when Jeremy Clarkson referred to facial growths as 'really ugly things' and said 'I'm talking about a growth', the Committee considered that this remark had a broader meaning than solely referring to the film character."
The Trust took into account the audience expectation of Top Gear's "banter and irreverent style of humour", and said that it was not putting disability off limits for humour.
However, it found that the remarks were "purposeless stereotypes" and therefore could cause offence.
"This is an area where producers should bear in mind that research has shown that public sensitivities are high and therefore care has to be taken. Judgements in this area are very fine," the Trust said.
"The Committee acknowledged that in this case the wording had been pre-scripted and the editorial team had exercised forethought. However, the decision had been on the wrong side of the line."