The girl was rushed to Royal Children's Hospital after being dragged barely alive from the Yarra River. The hospital said she died about four hours after the fall.
The father had appeared before a family court on Tuesday and Wednesday to settle custody of the couple's three children with their mother, a court official said.
The girl's two brothers may have been inside an SUV parked nearby when the man allegedly dropped the girl off the West Gate Bridge, Detective Inspector Steve Clark told reporters.
The surviving children were still with their father when he was arrested about an hour later outside the family court, he said. None of the family were identified by authorities to protect the children's identities.
The alleged murder happened during rush hour on the bridge, an eight-lane freeway linking downtown Melbourne with the city's western suburbs.
Shocked witnesses called police to report seeing the girl being thrown from the bridge into the river shortly after 9 a.m.
A man "dropped (her) over the bridge" into the water, and police in a boat rescued the child about 10 minutes later, Clark said.
Clark said their mother had been informed but did not give details.
A court official, who declined to be named because she was not authorized to speak to the media, said the custody hearing over the children had ended Wednesday without a ruling because the parents had agreed to share access.
The hearing had been listed to resume Thursday, but neither parent had been expected to attend for a third day in court, she said.
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Associated Press Writer Rod McGuirk contributed to this report from Canberra, Australia.
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