Doohan died at at his Redmond, Washington, home with his wife of 28 years, Wende, at his side, Los Angeles agent and friend Steve Stevens said. The cause of death was pneumonia and Alzheimer's disease, he said.
The Canadian-born Doohan was enjoying a busy career as a character actor when he auditioned for a role as an engineer in a new space adventure on NBC in 1966. A master of dialects from his early years in radio, he tried seven different accents.
"The producers asked me which one I preferred," Doohan recalled 30 years later. "I believed the Scot voice was the most commanding. So I told them, 'If this character is going to be an engineer, you'd better make him a Scotsman'."
The series, which starred William Shatner as Captain James T Kirk and Leonard Nimoy as the enigmatic Mr Spock, attracted an enthusiastic following of science fiction fans, especially among teenagers and children.
They starred together for three seasons before US network NBC cancelled it because of weak ratings.
But the team was reassembled when the franchise hit the big screen. Star Trek: The Motion Picture was released in cinemas in 1979.
Doohan appeared in seven big screen episodes of Star Trek, and continued to voice the franchise's video games into the late 1990s.
When the series had ended in 1969, Doohan found himself typecast as Montgomery Scott, the canny engineer with a burr in his voice. In 1973, he complained to his dentist, who advised him: "Jimmy, you're going to be Scotty long after you're dead. If I were you, I'd go with the flow."
"I took his advice," said Doohan, "and since then everything's been just lovely."
He came to embrace his Scotty character and attended Star Trek fan conventions into his 80s, before falling ill.
Doohan became a father again at the age of 80, when his wife gave birth to daughter Sarah.
His last public appearance was in October 2004 when he received a star on the Hollywood Walk of Fame.