The ban, which takes effect at 11.30 p.m. (0330 GMT Friday), does not affect cargo flights.
The rules apply to Canadian citizens and foreign nationals.
Health Minister Patty Hajdu said that although India only accounts for 20% of recent air travel volumes to Canada, over 50% of all positive tests conducted at the border are from the South Asian country.
"Given the higher number of cases of COVID-19 detected in air passengers arriving into Canada from India and Pakistan, Transport Canada is issuing a Notice to Airmen, or NOTAM, to halt direct passenger air traffic from those countries", said Transport Minister Omar Alghabra on Thursday.
Even in that case, you will have to quarantine at a hotel.
The United Kingdom has added India on the red list countries.
India recorded almost 300,000 new cases of COVID-19 on Wednesday alone, with 2,000 more deaths linked to the virus.
Brampton-based Punjabi language journalist Gurbhej Sidhu recently revealed the story of a young woman arriving at Pearson from India and going to her home with 13 other people.
China's Xi to attend online Biden climate summit
Greenpeace UK's head of climate, Kate Blagojevic, said the summit had more targets than an archery competition. Chinese President Xi Jinping delivers a speech at the Great Hall of the People in Beijing on October 23, 2020.
The Ministry of Civil Aviation had air bubbles with at least 27 countries which was a temporary arrangement between two nations, allowing commercial passenger services when regular global flights are suspended as a result of Covid-19.
British Columbia's provincial health officer said it's a hard time for not just people in India but those living here who have family and friends in that part of the world.
"We will be doing further analysis because it's an emerging situation, not just because of the variant of interest at this point but because they have unfortunately a very massive resurgence in that country", she said.
India posted the world's biggest one-day jump in coronavirus cases ever as a ferocious new wave grips the country, overwhelming hospitals and crematoriums and prompting frantic cries for help on social media.
Each of those infected people in turn have been out in the community spreading COVID but none of those resulting cases will be counted as resulting from travel, they will be community spread.
Pakistan's government warned this week that major cities might be closed if COVID-19 cases there keep growing.
Effective April 24, 2021 and for the next 10 days, Emirates flights from India to the UAE will be suspended.
At least 55 cases of the new variant first detected in India have been recorded by Public Health England in the latest week to April 14.
According to the spokesperson of the PIA, all the flights to Canada have been canceled due to the ban on flights from Pakistan to Canada.