Part of the upper right side of the bus was shorn off in the collision, which happened shortly before 4pm (5am Saturday, Singapore time) at a busy transit station in the west end of the city.
Mayor Jim Watson said two of the dead were riding the bus and one was on the platform at Westboro station, a major stop on the city's busway.
Investigators worked through the night and identified the three victims and contacted their families, said Const. Amy Gagnon.
She says their names will not be released at this time.
OC Transpo also tweeted about the crash, saying they were "keeping all those affected by the tragedy at Westboro Station today in our thoughts and prayers".
During a press conference, Ottawa Police said the bus driver had been taken into custody.
She said Ottawa police's collision investigation unit remains on the scene as it continues its examination of the collision.
Jurgen Klopp provides Joel Matip and Dejan Lovren updates amid injury crisis
They have not managed so far to topple any of the top four, Liverpool , Manchester City , Spurs and Chelsea. It's our situation, it's not that we made a decision to go out of the cups.
Ontario Premier Doug Ford said: "Devastated to hear about those who lost their lives and were injured following the horrific bus collision at Westboro Station in Ottawa".
Buses are being detoured as a result of the crash, OC Transpo said.
"This will be a long investigation", Bordeleau said. "And there was a bit of blood on the floor", Bilal Gill said.
"The bus started swerving, I guess it hit the curb or hit something".
"There's no question that the weather adds complexity at the scene", said Bordeleau said. The first seats on the upper level of the bus were crushed together. "There was definitely people pinned".
OC Transpo has been struggling with a bus driver shortage and chronic service problems as they transition from busses to the new, delayed LRT line.
The family reunification centre at the Churchill Seniors Centre has since been closed, but people seeking information about family members involved in Friday's crash can call the Canadian Red Cross at 1-855-797-8875.