The man has been in isolation at a Toronto-area hospital since Friday after complaining of fever, headaches and muscle pain.
However, Ontario Minister of Health Eric Hoskins said tests showed the patient did not have Ebola.
"I can now confirm a recent case that underwent testing at the National Microbiology Laboratory in Winnipeg was found to test negative for Ebola virus disease," Hoskins said in a statement.
Hoskins praised the prompt isolation of the individual at the first sign of possible Ebola infection.
"Our system worked as it should," he said.
The current outbreak of Ebola in West Africa is the worst in history, killing close to 1,000 people in the region since the start of the year.
The World Health Organization declared the epidemic an international health emergency on Friday.
States of emergency have already been declared in Guinea, Liberia, Sierra Leone and Nigeria.