The three left earlier Friday on a chartered plane to make the trip home. A quarantine officer assessed them when their plane landed in an undisclosed Canadian location.
They were deemed healthy and allowed to travel to private residences where they will enter a period of isolation.
The Public Health Agency has not released the names of the team and won't say where they live, for privacy reasons. They are believed to be employees of the National Microbiology Laboratory in Winnipeg.
Their mission was cut short over concerns for their safety when three people working at or staying in their hotel complex tested positive for Ebola.
One of the people was a Senegalese epidemiologist who, like the Canadians, was in Sierra Leone working under the aegis of the World Health Organization's Global Outbreak Alert and Response Network. The man was evacuated to Hamburg, Germany for care.
The WHO has temporarily shuttered the operation where he and the Canadians worked as it investigates how he contracted the disease.
The unit, which was based at Kailahun in eastern Sierra Leone, provided contact tracing and social mobilization services for the area. The mobile laboratory the Canadians operated supported a nearby Ebola treatment centre run by Medecins Sans Frontieres (Doctors Without Borders).
The U.S. Centers for Disease Control also withdrew two people from the Kailahun operation in response to the same situation. One of the CDC employees, an epidemiologist, had worked in close proximity to the Senegalese epidemiologist.
The CDC described the exposure as low risk, saying the two worked together in an office-type space.
The CDC said its scientist was due to return to the U.S. anyway, so the agency decided to bring the individual home. A second CDC person was approaching the end of a mission as well, so both were flown back to the U.S. on a private jet.
The WHO has asked people who are contacts of confirmed cases not to fly on commercial flights while they are in the incubation period of the disease.
The Canadians will isolate themselves — even from their families — as they wait out a 21-day incubation period. Their health will be monitored during that time, the agency said.
If they develop symptoms during that period they will be transported to hospital for assessment.
The Public Health Agency has said it remains committed to the effort to control the Ebola outbreak in West Africa and will send another team to restart the lab operation at Kailahun after appropriate steps are taken to ensure a safe living environment for the scientists.
It was revealed Friday that the outbreak, which has been raging for months, had breached another border.
Senegal announced it had diagnosed a case in a man who had crossed into the country from neighbouring Guinea, where the outbreak is believed to have begun.
Most cases have occurred in Guinea, Sierra Leone and Liberia, though Nigeria is working to contain an outbreak that began when an infected man from Liberia travelled there for a conference.
The WHO says there have been more than 3,000 cases and 1,550 deaths. It projected this week that as many as 20,000 people may be infected before the outbreak can be brought under control.