Armed police who had surrounded the house in Catford, south-east London, were told of the deaths by the couple's son, Hailly, aged four, who had been in the house during the shooting. None of the couple's three other children were hurt.
Police were alerted by Marcus, 11, who rang to say his mother's boyfriend, Calvert Summerville- Jones, had arrived.
When officers arrived they saw the man, who had a gun, and Doreen Henry struggling in an upstairs window. The police withdrew when they heard a shot and called for assistance. Two more shots were heard and a fire began in the back of the building.
A Scotland Yard spokeswoman said officers knew that two children, Hailly and Nicole, a baby, were in the house. Another daughter, Marsha, 17, was not there. Fire officers had just arrived when two more shots rang out. Hailly then came out crying, to say his parents were dead.
It is thought Ms Henry moved to Catford from Birmingham about two months ago to get away from Mr Summerville-Jones.