The crash happened just before 10 p.m.
The bus, from First Baptist Church Hillsboro in Coconut Creek, was bringing 25 passengers back from a water-park outing in Orlando.
Late Saturday, one seriously injured person had been airlifted to Delray Medical Center and eight others had been taken to Delray, West Boca Medical Center and Boca Community Hospital.
One person was still missing, according to the Florida Highway Patrol, and divers were searching the canal.
FHP Lt. Pat Santangelo said both the bus and a Ford Expedition were southbound on the turnpike when the Ford got a flat tire. Its driver lost control and bumped the bus, which was in the left lane.
The bus lost control, swerving to the right and over about a six-foot drop into the canal.
It was a section of the turnpike where the canal is not protected by a guardrail, Santangelo said.
The bodies lay on the west side of the canal, side-by-side and covered with plastic.
He said it was unknown if the three people killed were children or adults.
At one point, a near-hysterical woman ran up to the west bank of the canal, crying, "My son was on that bus!"
As a Palm Beach County sheriff's deputy consoled her, she looked up to spot her son on the other side of the canal.
"Greg!" she yelled.
But with the noise and commotion, her son could not hear her. She ran back to her car in an attempt to get onto the turnpike side of the road.
Sylvia Williamson, the wife of the Rev. Jerry Williamson, the church pastor, said 26 people were on the bus. Most of them were young people from the church youth group, in grades 7 to 12, she said.
According to Williamson, a motorist in a SUV was driving behind the church bus packed with youth group members when it blew a tire, swerved and slammed into the bus, sending the bus into the canal.
Church members riding in a van that was in front of the bus immediately called the Williamson home to let them know an accident had occurred.
"They said, `Pastor, we want you to know there's been an accident. The bus is submerged,'" Williamson said. "One of our youth pastors kept diving into the water and pulling people from the bus."
"It was the last hurrah before school starts," Williamson said, her voice faltering.
She said her husband, the pastor, initially was going to head to the accident scene but was told instead to go to West Boca Medical Center where victims were being transported.
"We just don't know anything yet," his wife said.
The church, at 5100 W. Hillsboro Blvd., has a small congregation of about 550.
She said the accident has hit them hard.
The scene alongside the canal, which flows between the turnpike and Boca Rio Road, was ordered chaos within minutes of the crash.
The white top of the school bus gleamed beneath about 8 inches of water in the canal. The bus sat upright, its pop-up roof hatch open with divers peering in the top and swimming below.
Helicopters hovered above the scene while the red-and-blue lights of more than 25 emergency vehicles lit up the night.
Traffic in both directions of the turnpike was shut down.
On the turnpike side of the canal, medical teams treated dazed, wet survivors, while TraumaHawk helicopters lifted off with other victims.
Staff Writer Sallie James contributed to this report.
