Air Canada said Flight AC7664, operated by regional partner PAL Airlines, was traveling from Newark, New Jersey, to Halifax, Nova Scotia, with 61 passengers on board when the first officer took control of the aircraft and diverted it to Boston, where it landed safely.
The captain was taken to a hospital for treatment, the airline said.
Rodney McDonald, who was traveling with his wife and two sons, recounted the frightening experience to ABC News, saying he knew something was wrong when the aircraft suddenly swerved.
"The moment the plane swerved, I knew something was wrong because it was not turbulence," he said. "It really felt like someone had jerked the controls, and then it happened over and over again. Every thought goes through your mind. You start praying. My boys instantly started praying."
McDonald said he watched a flight attendant rush into the cockpit before helping remove the captain into the aisle, a procedure Air Canada said is part of its safety protocols.
According to McDonald, the captain appeared to be having a seizure. He and about four other passengers helped restrain him while the first officer flew the aircraft to Boston.
"[We] worked to get him under control. It was a fairly strenuous 40 minutes of keeping him down and using as many seatbelts as we could to restrain his legs, arms and chest," McDonald said.
A registered nurse on board also helped direct passengers and assisted the captain throughout the ordeal.
Air Canada noted that pilots are trained to fly aircraft and land safely without the assistance of a second pilot.