Some who stayed behind huddled near pillars in Nathan Phillips Square even as the team and several dignitaries - including Prime Minister Justin Trudeau - remained on stage. Crowds gathered in the center of the city to celebrate the team's victory, and when shots rang out, swarms of people ran for cover.
The four people injured suffered non-life-threatening injuries.
The city's police said on Twitter that they recovered two firearms from the scene.
"We won't let this act of violence take away from the spirit of today's parade", he said.
"When we look at the casings that identify that a gunshot has occurred, they're not matching right now, on first blush, the guns we have seized".
The suspect wanted is described as a man about 5-foot-9 with a heavy build and short brown hair, who was wearing a white shirt. Police are still looking for a third firearm, the one they say was used to shoot at the event.
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Police have charged 18-year-old Abdikarim Kerow, 25-year-old Shaquille Anthony Miller and 20-year-old Thaino Toussaint. All three appeared in court Tuesday.
The men each face seven charges that include carrying a concealed weapon and - in Miller's case - assaulting a peace officer while carrying a weapon.
On Monday, Toronto police asked the public for their help in the shooting investigation.
Toronto police have charged three men and are looking for a fourth suspect after Monday's shooting that sent dozens scurrying for cover during a celebration for the Raptors' historic National Basketball Association win.
Toussaint faces four weapons-related charges, two counts of possession for the objective of trafficking and possession of the proceeds of crime.
Kerow faces 14 firearms charges and drug possession charges, for both OxyContin and cocaine, for the goal of trafficking.