Elton and Sheila reconciled in April this year after the singer faced a "potentially deadly" bacterial infection which left him "violently ill" on a flight to Chile from the UK.
"So sad to say that my mother passed away this morning", he wrote on Instagram alongside a photograph of the two of them.
He added: "Thank you for everything".
John said he last saw his mother a week ago and is "shocked" by her death.
The milestone birthday prompted Sir Elton to get back in touch, and the pair continued to work on their relationship. Stanley Dwight, who died in December 1991, never saw his son perform.
Mobile payments on Target with 'Wallet' debut
Folks will also be able to add their Target gift cards to Wallet, but again, the retailer did not say when that would be enabled. Currently, Wallet is only open to those who have the Target REDcard, but the feature will roll out to non-cardholders soon.
Google Maps introduces,'Two-wheeler', mode as an India first feature
If you're in India and want to try out the new two-wheeler mode, hit the button below and update your app. Google says that more countries around the world will see the mode, but hasn't shared which ones yet.
Netflix's Sci-Fi Series Altered Carbon Gets A Gorgeous, Epic, & NSFW Trailer!
Altered Carbon comes out on February 2 and is based on the cyberpunk novel from Richard K. The first season, which consists of 10 episodes, will premiere February 2, 2018.
Elton had only been back on speaking terms with his mum for a couple of years before she died. "Out of respect for my mother's privacy, I have always shied away from speaking publicly about our relationship".
In May, John had shared a throwback photo of himself and his mum with the message: "Dear Mum, Happy Mother's Day!".
When Sheila refused to do so during their telephone conversation, Elton broke off contact with her. Bob is like a son to me. I interviewed him last week for a magazine. And he banged the phone down.
The Sun said: "Elton ... failed to show up to his stepfather's funeral in 2010 and Sheila furthered the feud by hiring an Elton John tribute act for her 90th birthday party". I don't hate my mother. but I don't want her in my life'.
"At one point it was touch and go as to if I'd even be here".