The boy's mother, Tanita Brenssell, told the inquest she blamed Thompson, her former partner, for the death of her baby boy.
Thompson had reportedly taken on increasing responsibility for Israel's care in the months leading up to his death. He was the last person to see the boy alive.
The night before Israel's death, he showered with Israel and told the boy's mum that Israel "had a tumble in the shower" and was "a bit whingy".
Hours later, paramedics arrived to find Israel with blood on his face, bruising around his eyes and a swollen area on his head. They found him cold to touch.
There is no definitive cause of death but pathologists found Israel had been injured at least twice before his death and may also have asphyxiated.
"I believe strongly in my head and my heart that he's suffocated Israel, or he's done something along those lines," the mother told the coroner.
Thompson was due to give evidence at the inquest via video link from New Zealand, where he now lives, but didn't appear after receiving last-minute legal advice.
Outside court, Brenssell said she was hoping to get "closure".
"It's been a while," she said. "I'm hoping I can just have closure and move forward. And have that sense of peace with me again."
The grieving mum said Israel was "fun, very well behaved" and "a typical younger brother just trying to get in amongst the action".
"He loved to blow kisses. He liked reggae music. A beautiful spirit."
- With AAP
