Police said they learned of the deaths after responding to a midday (1700 GMT) medical call at the Sherman's home in an affluent section of northeast Toronto. Two bodies covered in blankets were removed from the home and loaded into an unmarked van on Friday evening.
"The circumstances of their death appear suspicious and we are treating it that way," said Constable David Hopkinson. Homicide detectives later told reporters gathered outside the home that there were no signs of forced entry.
Their neighbors, business associates and some of Canada's most powerful politicians said they were saddened by the deaths.
"Our condolences to their family & friends, and to everyone touched by their vision & spirit," Prime Minister Justin Trudeau wrote on Twitter.
Toronto Mayor John Tory said in statement he was "shocked and heartbroken" to learn of the deaths, noting that the couple had made extensive contributions to the city.
"Toronto Police are investigating, and I hope that investigation will be able to provide answers for all of us who are mourning this tremendous loss," Tory said.
The Shermans recently listed their home for sale for nearly C$7 million ($5.4 million). A real estate agent discovered the bodies in the basement while preparing for an open house, the Toronto Globe and Mail reported, citing a relative.
Sherman, 75, founded privately held Apotex in 1974, growing it by introducing large numbers of low-cost generic drugs that took market share from branded pharmaceuticals. He stepped down as chief executive in 2012 but remained executive chairman.
Forbes has estimated Sherman's fortune at $3.2 billion.
Apotex is the world's No. 7 generic drugmaker with 11,000 employees and annual sales of more than C$2 billion in more than 45 countries, according to its website.
The couple was known for their philanthropy, giving tens of millions of dollars to hospitals, universities and Jewish organizations, CBC reported.
"They were extremely successful in business, but also very, very giving people," former Ontario Premier Bob Rae told CBC. "It's going to be a very, very big loss."
The Globe and Mail reported in February that Lobbying Commissioner Karen Shepherd was investigating a complaint about a 2015 political fundraiser that Trudeau had attended.
(Writing and additional reporting by Julie Gordon in Vancouver; Editing by Jim Finkle, Leslie Adler and Paul Tait)
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)