Detectives had been investigating reports that Mr Partington had rowed with his girlfriend Tanya Williamson, just hours before the explosion.
He was so badly hurt in the blast that he has remained in hospital ever since.
But prosecutors today announced that he was to be charged with manslaughter and causing criminal damage valued at over £1 million.
Chief Crown Prosecutor for CPS North West Area, Nazir Afzal said: "I have today advised Greater Manchester Police to charge Andrew Partington, 26, with the manslaughter of Jamie Heaton, aged two, and causing criminal damage valued at over £1m to houses in Buckley Street, Shaw, Oldham, on 26 June 2012.
"Police were called to the scene of a gas explosion in Buckley Street at around 11.15am where two houses, number nine and number 11, were destroyed in the blast and other homes damaged.
"The seat of the blast was in number nine and Jamie, who was in the living room of his home at number 11 watching television, died as a result of the explosion. I would like to express my sympathy to Mr and Mrs Heaton on their tragic loss.
"After considering the evidence, I am satisfied there is sufficient to charge Andrew Partington with manslaughter and criminal damage. The decision was taken in accordance with the Code for Crown Prosecutors."
Mr Partington is due to appear before Oldham Magistrates later today.