Spokesman Jeff Mann says it happened Monday afternoon at the facility in Fort Saskatchewan.
He says the upgrader had to increase flaring in order to shut down the unit in a controlled manner.
Mann says Shell was monitoring air quality and testing showed sulphur dioxide levels were below guidelines.
Mann says there is no health risk for residents.
An employee was brought to hospital, but Mann says the health concern was unrelated to the problem with the sulphur unit.
Mann said no workers were sent home and there were no evacuations of residents.
He also said the all-clear was signalled about four hours after the incident and the plant was running as normal.