The weather service issued the warning around 2:40 p.m., saying forecasters were watching for a storm capable of bringing heavy rain and hail.
The “quasi-stationary severe thunderstorm” was located near North York.
Environment Canada warned that in addition to large hail, Torontonians could expect more than 50 millimeters of rain in an hour.
Other areas of the GTA, including North York and Vaughan, may also be affected.
Environment Canada urged residents to “cover up immediately” if the weather approaches, as heavy rains can cause flash flooding and pooling of water on roads.
By 3:00 p.m. the severe storm warning had expired.
Temperatures in Toronto are expected to rise to around 27 degrees Celsius, with temperatures reaching 31 degrees with humidity. There is a 30 percent chance of showers continuing into the early evening.
Environment Canada is also forecasting showers Thursday afternoon, with a risk of thunderstorms.