The 'Fire With Fire' group, who opened the month-long festival in London last night, gave a shout-out to John, who was seen viewing the performance from a VIP balcony.
Before they launched into the track, NME reports frontman Jake Shears announcing: "We want to dedicate a real sweet song for a dear friend of ours who is here tonight. This is for you Elton, we love you."
The song was co-written by John, and reached number one of the UK singles chart in 2006.
Ana Matronic also praised rockers The Drums, who played earlier that night.
She said: "I love those boys from The Drums, they are so fantastic. They are our homeboys from Brooklyn and I've tasted each and every one of them."
The Scissor Sisters new album Night Work is out now.