"We will always speak up for human rights, we will always speak up for women's rights around the world", she told reporters in Vancouver.
It is unclear what, if any, implications the move has for existing trade ties between the two countries.
Saudi Airlines reportedly suspended flights to Canada, and some 12,000 Saudi citizens studying at Canadian universities were being moved to "programs in other countries with similar education systems, such as the United Kingdom", according to the Canadian newspaper the Globe and Mail.
But Canada has stood firm, with Foreign Minister Chrystia Freeland insisting it would defend human rights around the world.
But Riyadh's singling out of Canada is aimed at strongly discouraging other critical Western governments from speaking out, observers say.
In an earlier response to Freeland's tweet, the Foreign Ministry of Saudi Arabia issued a statement ordering Canadian Ambassador Dennis Horak to leave the country within 24 hours.
The Saudi government on Sunday recalled its ambassador to Ottawa, barred Canada's envoy from returning and placed a ban on new trade, denouncing Canada for urging the release of jailed rights activists.
Saudi's foreign ministry called the statement "a major, unacceptable affront to the kingdom's laws and judicial process". Saudi authorities accused Ottawa of interfering with its internal affairs. Media reports also suggest Saudi Arabia may cancel thousands of scholarships for students attending school in Canada.
On Monday, Saudi Foreign Minister Adel al-Jubeir criticized Canada's calls to free arrested civil society activists as a position built on "misleading" information. Raif Badawi, who won Europe's top human rights prize in 2015, was later sentenced to 10 years in prison and 1,000 lashes for insulting Islam while blogging.
At the same time, it sends a strong message to European and Middle Eastern countries not to "mess" with Saudi Arabia, Juneau said.
"We're going to stand with the values that we know are important to Canadians and Saudi Arabia will take the decisions that they take", Morneau said.
"I don't think it will worsen the situation because very often when we make evident unjust imprisonments, like the case of Samar Badawi, that increases their protection and increases pressure on the government", she said in an interview Monday.
The Twitter account has been described as "an official government" account in Saudi-owned state media, although the relationship to the Saudi state is not clear.
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