The government of British Columbia (BC) says the requirement is discriminatory as well as being a health and safety issue because they are dangerous.
It says that high heel wearers face a risk of physical injury from slipping or falling as well as possible damage to the feet, legs and back.
Footwear should be designed to allow workers to operate safely, it says.
The announcement of the ban comes after a provincial Green party politician in March introduced a bill in the BC legislature aimed at preventing employers from setting gender-based footwear requirements.
BC Green Party leader Andrew Weaver filed a private member's bill "designed to prevent employers from setting varying footwear and other requirements based on gender, gender expression or gender identity".
His bill covered all workplaces, including retail and corporate offices. But instead of implementing it, the provincial government opted instead to amend footwear rules under the Workers' Compensation Act.
BC Premier Christy Clark said that in some provincial workplaces, women were unfairly required to wear high heels.
"Like most British Columbians, our government thinks this is wrong. That is why we're changing this regulation to stop this unsafe and discriminatory practice," she said.
The new regulation states that workplace footwear must be of "a design, construction and material that allows the worker to safely perform their work and ensures that employers cannot require footwear contrary to this standard".
The new guidelines, drafted by WorkSafeBC, are expected to be available by the end of April.
High heels - and whether women should be required to wear them in the workplace, or at the Cannes film festival - has become a fashion flashpoint in recent years.
In Canada, much of the debate around dress codes for female employees has centred around the restaurant industry, where critics have said gender-specific dress codes are too common and based on stereotypes or sexist ideas of how a woman should dress.