Teacher Jason Lees apparently then took his own life by throwing himself off in the early hours of the morning.
Lees, 40, is thought to have leapt from the Story Bridge in Brisbane, Australia, after reportedly stopping his bicycle on the footpath before flinging his son over the safety rail.
Cops refused to say whether he was in a custody battle.
Lees taught at an exclusive school in the city where his headmaster Jonathan Hensman said it was a day of "shock and sadness".
He added: "He was an outstanding teacher and very generous contributor to the whole of our programme, not just the classroom, which of course adds to the shock of the circumstances surrounding this."
The incident comes five months after a mentally-ill woman committed suicide at the same spot having killed her teenage daughter.
Three years ago a 37-year-old man threw his four-year-old daughter off Melbourne's West Gate Bridge as he fought for custody of the girl.