John Cooper and his wife Susan lost their lives within hours of each other at Aqua Magic hotel in the Red Sea resort town of Hurghada on 21 August.
A public prosecutor in Egypt confirmed the lethal bacteria was a factor in the tragic couple's demise as he detailed an official medical report.
An inspection of the couple's hotel room revealed there were no toxic or harmful gas emissions or leaks but prosecutor Nabil Sadek said forensic tests showed John, 69, suffered acute intestinal dysentery caused by E.coli.
Susan, 64, had suffered Hemolytic-uremic syndrome (HUS), likely because of E.coli.
Thomas Cook had already confirmed high levels of E.coli were found in food at the Egypt hotel where the couple died.
The travel giant revealed the results of independent tests conducted at the Steigenberger showed the presence of the food poison bug – as well as bacteria linked to sepsis and deadly toxic shock syndrome.
Experts analysing food and hygiene standards at the resort identified a high level of E.coli and staphylococcus bacteria.
The couple, from Burnley, Lancs, died within hours of each other at their Hurghada resort.
Their deaths were initially recorded as being down to heart and respiratory failure — but a postmortem proved this not to be the case.
The bodies have now been released for repatriation by the Egyptian authorities and once the bodies are back in the UK, authorities here will carry out their own post-mortem.
Egypt's ministry for tourism released a statement saying it hoped the post-mortem result would help the grieving family come to terms with the "tragic loss" and "end speculative suggestions".
John, 69 died in his room after collapsing on his bed, while wife Susan, 64, was rushed to hospital but later succumbed to the then mystery illness.
A spokesperson for Thomas Cook said: “Thomas Cook notes the announcement today by the Egyptian prosecutor on the results of the autopsies of John and Susan Cooper following their deaths at the Steigenberger Aqua Magic in Hurghada on 21 August 2018.
"We have not yet seen the full report and we will need time for our own experts to review it.
“We are deeply saddened by the tragic deaths of John and Susan Cooper. We will continue to offer every support to their daughter Kelly and the rest of their family.”
Following the deaths Thomas Cook moved 300 customers out of the hotel.
Escherichia coli is a type of bacteria common in human and animal intestines.
While most types of E.coli are harmless some can cause serious food poisoning and infection.
Some E.coli strains produce toxins (Shiga toxins) that can cause severe illness.
A particular life-threatening complication called haemolytic uremic syndrome (HUS) may develop in 5-10 per cent of people infected with a toxin-producing form of E.coli.
This is a severe kidney-related complication that may, in extreme cases, lead to renal failure and the need for renal replacement therapy.
Egypt's tourism minister Dr Rania al-Mashat said: "The autopsy reports published today by Egypt’s Attorney General Nabil Sadek are one more step forward towards helping the grieving Cooper family come to terms with the tragic loss of John and Susan.
"The causes of death, e-coli bacteria, were medically determined by a team of internationally accredited pathologists, which I hope for the family’s sake will put an end to previous speculative suggestions of what might have happened.
"The health and safety of all tourists to Egypt are absolutely paramount and I am determined, together with the Prime Minister Dr Mostafa Madbouly and our fellow Ministers to ensure the highest standards of well-being for all visitors to our country.
"We will review the Attorney General’s autopsy reports in fine detail to determine our next course of action to look after the welfare of our visitors."
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