The world record holder was barracked by the Rio crowd when attempting to jump 6.08 metres to stay in the competition against Thiago da Silva, who sprung a huge surprise by winning Brazil's first athletics gold of the Games in the event.
Lavillenie gave the partisan crowd a thumbs down at the start of his run-up in attempt to get them to stop the jeers and said after failing to clear the bar that it was a "bad look" for the Olympics.
"In 1936 the crowd was against Jesse Owens," he said of the black American sprinter whose four gold medals in Berlin were an affront to the Nazi ideology of racial superiority.
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"We've not see this since. We have to deal with it."
On Tuesday, however, Lavillenie accepted that it was an inappropriate reference.
"Yes, sorry for the bad comparison I made," he said on Twitter. "It was a hot reaction and I realise it was wrong. Sorry to everyone."
(Reporting by Nick Mulvenney, editing by Clare Lovell)
