The ban would apply to countries with "widespread and persistent-intense transmission", Canada said.
The WHO said on Friday that 4,951 people had died during the current outbreak, with 13,567 reported cases up to 29 October.
Although Canada currently has no cases of Ebola, the country's federal citizenship ministry said "the introduction or spread of the disease would pose an imminent and severe risk to public health".
David Fidler, a professor at Indiana University in the US, told Canadian media that the government's move undermined international regulations drawn up after the Sars outbreak of 2003.
The judge said Kaci Hickox did not need to be isolated or restricted in her movements because she is not showing symptoms of the virus.
The vaccine, jointly developed by US disease authorities and pharmaceutical firm GlaxoSmithKline, is already being tested on volunteers in the US, UK and Mali.