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1 year oldAfter first resisting calls to step down, Anthony Rota quit on Tuesday after meeting party leaders in Ottawa.
"I must step down as your Speaker," he said in parliament. "I reiterate my profound regret."
The incident last Friday incited global condemnation.
Yaroslav Hunka, 98, got a standing ovation after House of Commons Speaker Anthony Rota called him a "hero" during a Friday visit by Ukraine's president.
Mr Rota has said he did not know of Mr Hunka's Nazi ties and made a mistake in inviting him to attend the event.
Canada's Prime Minister Justin Trudeau said on Monday it was "extremely upsetting that this happened".
"This is something that is deeply embarrassing to the parliament of Canada and by extension to all Canadians," he told reporters.
Members of Mr Trudeau's cabinet had joined cross-party calls for Mr Rota to step down.
Hours before the Speaker announced his resignation, Foreign Affairs Minister Melanie Joly called Mr Hunka's mistake "completely unacceptable".
"I think the Speaker should listen to members of the house and step down," she said. "I don't think there's any alternative."