John Meek and April Keeling, from Cannock, had always denied the findings of the original inquest into their three-year-old son's death in 2014, which ruled that pneumonia was the cause.
Those findings were quashed by the High Court and a new inquest took place in Shrewsbury this week.
Coroner John Ellery heard that Jonnie was taken into Stafford Hospital on August 11, 2014, for a pre-arranged trial of a feed solution, Peptamen Junior Advance.
Jonnie lived with the rare condition De Grouchy Syndrome, had asthma and various dietary intolerances. He could not keep many kinds of feed down and would not put weight on.
At 1.30pm on August 11 he was administered Peptamen, which he had been given on a previous occasion in a higher dosage and reacted badly to.
On the second occasion, April noticed a decline in his condition after he was given the feed and tried to get the attention of medics. He developed a rash, breathing problems and parts of his body turned purple.
Despite the efforts of doctors and nurses, including resuscitation, he died soon after 4pm.
The inquest this week heard from those who had helped care for Jonnie, as well as three experts who examined the case including the doctor who had carried out the initial post mortem.
Despite some initial disagreement, the experts, Dr Tomas Marton, Dr Andreas Marnerides and Dr Donald Hodge, all came to a consensus that Jonnie's death was caused primarily by the breathing problems stemming from the feed solution.
After hearing all the evidence, Mr Ellery recorded that the primary or 1a cause of death was "adverse reaction to introduction of the new feed". A contributing factor, the 2 cause, was "De Grouchy Syndrome, severe developmental delay, chronic lung damage and pneumonia".
He said that the doctors' findings vindicated what John and April had always believed – that their son died because of the change of feed and not of "unrelated, natural causes".
More from the inquest:
In his narrative he said: "Jonnie William Meek died following, and as a result of, an adverse reaction to a change of feed."
He told an emotional John and April: "I can only describe you as Jonnie's devoted parents. You have fought and waited a long time, a very long time, for answers to your questions.
"I hope this inquest has in some part helped you to deal with your loss."
John and April thanked the coroner and all of the various groups that have helped them in their campaign over the last six years.
Among them was the region's Clinical Commissioning Group (CCG), whose representatives attended throughout the inquest.
Sally Young, director of corporate services and Heather Johnstone, director of nursing and quality at the NHS Staffordshire and Stoke-on-Trent CCG said: “The CCGs have supported Jonnie's family as they have fought, with exceptional dignity, to get answers to their questions about his death.
"We would like to pay tribute to the family's resolve and we hope that today's conclusion can allow them the find some peace.
"We would also like to thank the Coroner, Mr John Ellery, for the dignified way in which he has conducted this inquest.
"The local NHS is a very different place now from what it was in 2014 and the CCGs have already acted upon recommendations arising from its own independent investigation report made following Jonnie’s death."