It followed a domestic incident in which Mrs Ege suffered a split lip, the court has heard.
Mr Ege denies a charge of causing the boy's death by failing to protect him.
Mrs Ege made a confession to police within days of Yaseen's death at their home in Cardiff in July 2010.
Police officer Andrew Williams described the moment Mr Ege was told by a doctor that his son was dead.
BBC: Yaseen Ali Ege death: Father Yousuf Ege 'unusually calm'
He said Mr Ege fell to his knees with a loud bang and started crying, calling out his son's name.
BBC: Yaseen Ali Ege death: Father Yousuf Ege 'unusually calm'
The jury heard how Mr and Mrs Ege were taken to hospital in a separate ambulance to their son, who was pronounced dead en route.
BBC: Yaseen Ali Ege death: Father Yousuf Ege 'unusually calm'
Earlier on Monday, Mr Ege cried as the court was shown a video of his son.
At the time of her murder, Mrs Ege's family said she was a gifted and talented teacher.
In a statement he said Sara Ege was clearly suffering from smoke inhalation.
BBC: Yaseen Ali Ege death: Father Yousuf Ege 'unusually calm'
Barach Bandavad, of Highbury Road, Horfield, was convicted of murdering Judith Ege, 58, and was sentenced to a life term.
Mrs Ege said in interview that Yaseen had collapsed in a similar way about six weeks earlier and had been fine after a night's sleep.
Unrecorded sections of interviews with Mrs Ege were also read out to the court by a police officer and one of the prosecution team's barristers, David Elias.
The teaching assistant said she did not know what was said in the head teacher's office, but dismissed a suggestion she was mistaken about Mrs Ege being asked to see her.
Mrs Ege is accused of hitting and punching Yaseen and punishing him using a hammer, a rolling pin and a slipper.
Mr Ege told Cardiff Crown Court on Tuesday the first he knew Yaseen had not died in a fire was when his wife told him he had collapsed on the day of the fire.
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