On Monday, the singer shared a photo of himself with Sheila Farebrother, writing: "So sad to say that my mother passed away this morning.
"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."
Ms Farebrother was 92 years old. Until recently, the pair had been out of touch because of a family rift.
In May, the singer posted a photo of the two on social media with the caption: "Dear Mum, Happy Mother's Day! So happy we are back in touch. Love, Elton xo".
At her 90th birthday party, Ms Farebrother hired an Elton John tribute act to perform.
Following the milestone, he reached out to his mother for the first time in seven years - sending her white orchids.
Recently, Sir Elton cancelled a series of forthcoming performances as he recovers from a serious illness that a spokesman described as "potentially deadly".