The bodies of Barry Sherman and his wife Honey were found in the basement, reports said.
Sherman was the founder and chairman of pharmaceutical giant Apotex, which sells generic medicines around the world.
He was one of Canada's richest men and a prominent philanthropist, reports BBC.
Police gave few details and did not confirm the identities of the deceased. However, they were named locally by friends and by officials who reacted with shock at the news.
"I am beyond words right now," Ontario's Health Minister Eric Hoskins said on Twitter.
"My dear friends Barry and Honey Sherman have been found dead. Wonderful human beings, incredible philanthropists, great leaders in health care."
A police spokesman said emergency services were called to the house just before noon on Friday.
"The circumstances of their death appear suspicious and we are treating it that way," said Constable David Hopkinson.
Apotex said in a statement: "All of us at Apotex are deeply shocked and saddened by this news and our thoughts and prayers are with the family at this time."
The couple had four children.
Sherman founded Apotex Inc in 1974 and the firm says it is now the seventh biggest drug maker in the world.
Forbes magazine puts Sherman's personal net worth at $3.2bn (£2.4bn).
