The bodies of Barry Sherman and his wife Honey were found in the basement by an estate agent, reports said.
Investigators are still attempting to "determine if there is foul play involved or not", Detective Brandon Price told reporters, "and at this point we can not say 100% with certainty if there is or there is not".
Staff Sgt. Jeff Taylor of Toronto police's 33 Division said officers were called shortly before noon to the home at 50 Old Colony Rd., near Bayview Ave. and Highway 401.
A local constable said the circumstances of the deaths appear to be suspicious and it is being treated as such. The pharmaceutical company produces and exports generic drugs to more than 115 countries.
There was no sign of forced entry to the property, police said in a statement Friday evening.
In a statement, Apotex confirmed the Shermans had been killed: "We've been informed of the tragic news that Barry and Honey Sherman have unexpectedly passed away".
One of two bodies is removed from the home of billionaire founder of Canadian pharmaceutical firm Apotex Inc
Forbes magazine estimated Mr Sherman's personal net worth at $3.2bn (£2.4bn), making him the 15th richest Canadian.
'Our condolences to their family & friends, and to everyone touched by their vision & spirit, ' Prime Minister Justin Trudeau wrote on Twitter.
Detective Brandon Price told Canadian broadcaster CBC that investigators were still trying to determine if there was foul play involved. "Patients around the world live healthier and more fulfilled lives thanks to his life's work". "As employees, we are proud of his tremendous accomplishments, honored to have known him, and vow to carry on with the Apotex objective in his honor".
"I am gutted by the loss of Honey and Barry Sherman". She also served on the boards of Mount Sinai's Women's Auxiliary, the Simon Wiesenthal Center and the International American Joint Distribution Committee.
Outside of the pharmaceutical business, the Shermans were also known for their philanthropy. The couple made numerous multimillion-dollar donations to hospitals, schools and charities and had buildings named in their honour. A listing posted online said the home is now on the market for just under $7 million.