The country also reimposed testing, warning that the Omicron variant of Covid-19 risks quickly overwhelming hospitals.
Apart from Nigeria, the travel restriction on flights is also lifted on South Africa, Mozambique, Botswana, Zimbabwe, Lesotho, Eswatini, Namibia, Malawi and Egypt.
Health Minister Jean-Yves Duclos was quoted as announcing this at a news conference on Friday.
He said the lifting of the travel ban would take effect from 11:59 pm on Saturday.
The restriction had been announced last month “to slow the arrival of Omicron in Canada and buy us some time,” he said.
“But with Omicron now spreading within Canada it is no longer needed,” he added.
Pre-arrival negative PCR tests for all travelers would also be reinstated as of December 21, Duclos said, while repeating a government warning earlier this week that “now is not the time to travel.”
Officials said laboratory tests have confirmed as of Friday nearly 350 cases of the Omicron variant across Canada.
The total average daily Covid case count, meanwhile, has jumped by 45 percent in the past week to about 5,000.
“It is expected the sheer number of (Omicron) cases could inundate the health system in a very short period of time,” said Chief Public Health Officer Theresa Tam.