The dinosaur-mad youngster, a pupil at Deri primary school, near Bargoed, Caerphilly, died from renal failure in the Bristol Royal Hospital for Children on Tuesday.
As TES Cymru went to press, another five children remained in hospital after developing E.coli poisoning, and the number of confirmed cases stood at 157 - spread across four local education authorities and involving 42 schools.
Public health officials this week said that the E.coli strain behind the outbreak had been found in cooked meat samples taken from John Tudor Son, the Bridgend meat supplier named as a possible source.
Last week, Assembly members questioned the decision to keep schools open when the first E.coli cases emerged in mid-September. But health minister Dr Brian Gibbons said that the decision had been the right one.
"Evidence shows that the advice of the outbreak control team to keep the schools open, and the control measures they introduced, were and are effective," he said.
"It appears there have been no new primary cases from the schools outbreak since September 26. There have been no secondary cases in schools, that is from contact with primary cases."
Schools were told to ensure children washed their hands, to serve only hot cooked meals at lunchtime, and to ban playing with sand and water to reduce the chance of spreading germs.
Dr Gibbons has asked the outbreak control team to identify any further actions that need to be taken to protect public health. Assembly members will agree the terms of reference for a public inquiry.
Mason had been in hospital for just over a week. His older brother Chandler, aged eight, contracted the bug several days before but is recovering at home.
Nicola Williams, acting headteacher of Deri primary, said: "Words cannot describe how much we will miss Mason. Our thoughts and love are with Mason's family at this time.
"He was mad about dinosaurs and made us all smile with the way he always seemed to turn any conversation into one with a dinosaur theme.
"He was a very special friend to all the children and was the kind of character who was a joy to have in school. None of us will ever forget him."