The song was served as an encore of a set that began with a cover of 'Que Sera Sera' to tribute the late singer and actress, Doris Day, who died at the age of 97 earlier this week.
Watch the full performance below.
Clapton also performed songs like 'Layla', 'Crossroads' and his cover of Bob Marley's 'I Shot the Sheriff' in his 17-song set.
Clapton explained that he discovered Prince's music during a particularly dark period of his life. A few days after his death in April 2016, Clapton wrote on Facebook, "I'm so sad about the death of Prince".
"He was a true genius and a huge inspiration for me, in a very real way. In the '80s, I was out on the road in a massive downward spiral with drink and drugs. I saw 'Purple Rain' in a cinema in Canada."
Clapton continued, "I had no idea who he was, it was like a bolt of lightning! In the middle of my depression and the dreadful state of the music culture at that time, it gave me hope. He was like a light in the darkness. I went back to my hotel and, surrounded by empty beer cans, wrote 'Holy Mother.' I can't believe he's gone."