The arguments sparked allegations of rhetorical excess from both sides and prompted European Council President Donald Tusk to finally enter the referendum debate, deriding Johnson's comments.
Tusk said that "when I hear the EU being compared to the plans and projects of Adolf Hitler I cannot remain silent."
"Such absurd arguments should be completely ignored if they hadn't been formulated by one of the most influential politicians of the ruling party," Tusk said in Copenhagen.
Britain holds a "leave or stay in" referendum on June 23 on its always cantankerous relationship with the EU, and the campaign has become increasingly edgy.
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In a speech today aimed at bolstering arguments for remaining in the EU, Cameron said "it is worth asking the question: Who would be happy if we left?"
He said Russian President Vladimir Putin "might be happy" and that he suspected IS leader Abu Bakr "al-Baghdadi might be happy."
Johnson countered that "it's a bit much ... To say our allies are Putin and Daesh," another name for the Islamic State group.
In Britain, the EU institutions and its leaders in Brussels have long been seen as the source of all things bad related to the bloc. Because of it, Tusk and others have taken a hands-off approach in a campaign that is also vital to the future of the EU itself.
"Boris Johnson crossed the boundaries of a rational discourse, demonstrating political amnesia," said Tusk.