Alex-Marie Quinn had 65 other injuries, pathologist Prof Rupert Risdon told St Albans Crown Court.
Carl Wheatley, 31, from Hatfield, Hertfordshire, denies murder but admits Alex-Marie's manslaughter.
Concluding the bruise led to her death, Prof Risdon told the court he had never seen such an injury.
Prosecutors have alleged Mr Wheatley lost his temper and beat his daughter to death with "sustained persistent hard hitting".  He had gained custody of her just a few months earlier.
Prof Risdon found 65 marks of injury across her body, head and arms but a "66th" area of bruising had caused Alex-Marie's death.
Bruising covered the lower body and legs from above her belly button ending shortly before her ankles, in the front and back.
Alex-Marie's soft tissue was damaged under the skin releasing a massive amount of fat cells into her blood stream, the court was told.
The cells then travelled to her lungs, blocking them and causing an embolism.
Prof Risdon said: "It's an unusual finding. I've never seen anything quite like it."
Jane Bickerstaff QC, defending, asked him to consider a "scenario" where the little girl had been repeatedly smacked over her clothing.
But, for a period of up to 36 hours before her death, she had not been hit anymore as she lay "moribund" on her mattress.
Prof Risdon said: "I find that scenario hard to accept because once the fat lodged in the lung the subsequent deterioration and demise would be fairly quick and not over a period of days."
Mr Wheatley denies murdering Alexa on 12 March 2014, but admits manslaughter on grounds of diminished responsibility.
A four-year-old died at the hands of her father after sustaining a "massive" bruise from her stomach to ankles, a court heard.