The singer tweeted that the 17-year-old "decided to end his struggle on the ground today."
Sharing the news on social media, the musician wrote that he had "decided to end his worldly struggle" and said that "no one follows his example".
On Thursday, when he went missing from the hospital, he tweeted directly to her: "This is a message for my son Shane. Shane, it's no longer ridiculous that all this is disappearing. You're scaring me with nonsense. Can you please do the right thing and present yourself at the rotation station? If you're with Shane, please call the guard to protect him.
"26 hours after my son's death in the form of Tusla in the so-called care of the Irish state," he tweeted, referring to the Irish Child Protection Service.
"I have not yet received any contact from Tusla or their representatives. I was informed of my son's death by the Guardia and later spoke to GAL. Any contact from Tusla is unacceptable."
It is unclear where and when Shane died. O'Connor called it the "light of my life".