The star revealed his loss in an emotional tribute posted to his Instagram account, saying that he was 'in shock' at her passing.
'So sad to say that my mother passed away this morning,' Elton, 70, wrote along an image of the pair together. 'I only saw her last Monday and I am in shock. Travel safe Mum. Thank-you for everything. I will miss you so much. Love, Elton.'
Followers have rushed to send Elton messages of condolence and support, with one writing: 'So sorry to hear your sad news 😞 may she RIP & my condolences to u & your family xx'
'So sorry Elton. All my love to you and your boys,' another agreed.
Elton and Sheila had a difficult relationship over the years, but had since managed to repair their bond, with the award-winning singer posting a sweet message for her on Mother's Day.
'Dear Mum, Happy Mother's Day! So happy we are back in touch,' Elton declared at the time.
Before they reunited, the pair had reportedly not spoken to each other since 2008, having cut off their communication after an argument.
'I've had all the upset and crying and the worrying and the nastiness. I've got over it now and I've got a nice life. And I just hope he's as happy as I am,' Sheila said during an interview with the Daily Mail in 2015.
Elton and his husband David Furnish are themselves the proud fathers to two sons - Zachary, whom they welcomed in 2010, and Elijah, who arrived in 2013. Both boys were born via surrogate.
Elton has since referred to his sons as his 'greatest decision'.
'If I was 15 years younger, I'd have two or three more. Without question,' he told Zane Lowe in March 2017.