Bishop Williamson, of the ultra-conservative breakaway Catholic group the Society of St Pius X, was dressed all in black, including sunglasses and a black cap, as he made his way through Ezeiza international airport in Buenos Aires to board a British Airways flight.
A man accompanying him manhandled a journalist who asked Bishop Williamson his destination and whether he would recant his views.
He refused to answer questions about his departure, which followed a decision last week by the Argentine government that his immigration papers were not in order and he should leave the country within ten days.
An interview in which the bishop questioned the scale of the Holocaust and the use of gas chambers was broadcast in the week the Pope cancelled his excommunication, sparking fury among Jewish groups.
The government of Argentina, where he had served as head of a seminary near Buenos Aires for the last six years, said that his comments "profoundly insult Argentine society, the Jewish people and humanity in general".
The British-born bishop is a member of the ultra-conservative Catholic group founded by the late Archbishop Lefebvre.
Father Richard Bouchacourt, the head of the Society of St Pius X in South America, told the Telegraph that he hoped that the scandal and attention it had attracted would now be over.
"This has damaged the society and it has damaged the Pope," he said.
He alleged that the timing of Swedish documentary in which Bishop Williamson made his comments that "between 200,000 and 300,000 Jews perished in Nazi concentration camps, but none of them by a gas chamber" had been deliberately designed to damage the Vatican.
The programme was broadcast to coincide with the Vatican's announcement last month lifting the excommunication of Bishop Williamson and three other priests consecrated by Archbishop Lefebvre, in a bid to heal the rift with church traditionalists.
Fr Bouchacourt added that despite the "media storm" created by Bishop Williamson's comments, talks between the society and the Vatican would continue.
The Pope has demanded that Bishop Williamson retract his comments before letting the four priests fully back into the church.
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