Connery's wife and two sons said he "died peacefully in his sleep surrounded by family."
Connery rose to global acclaim for his portrayal of British secret agent James Bond in 1962's "Dr. No," based on the Ian Fleming novel.
Connery continued as Bond in "From Russia With Love," "Goldfinger," "Thunderball," "You Only Live Twice" and "Diamonds Are Forever," often performing his own stunts.
Connery was also no stranger to San Francisco.
VIDEO: Sir Sean Connery, iconic James Bond actor, dies at 90
In fact, he was a big fan of the city and filmed the Alcatraz thriller "The Rock" there in 1996.
The actor plays John Patrick Mason, an aging British Special Air Service agent and the only man ever to escape from Alcatraz.
"Oh yes, its very nice favorable town," Connery told ABC7 News while on set in June 1996, "Fresh air. Good restaurants."
In Connery's middle age, the actor went onto star in movies including "Robin and Marian," "The Hunt for the Red October," and the "The Untouchables," for which he won an Oscar.
Connery is survived by his wife, brother Neil and sons Jason and Stefan.
His publicist, Nancy Seltzer, said there would be a private ceremony followed by a memorial service once the coronavirus pandemic has ended.