The legendary guitarist walked off stage part way through the penultimate song of the evening, Cocaine. He returned to play one final song, before leaving again.
Within minutes of Saturday night's concert ending angry fans, who paid around £60 for a ticket, took to websites including heraldscotland.com to express their anger. Several concertgoers also demanded refunds, saying they felt "let down and disappointed".
A spokesman for Clapton said he was "sorry for the break in the concert". She added: "Unfortunately, last night we experienced a steadily worsening technical problem with the PA system that the band battled with throughout the show but by the last song of the set it became unbearable on stage and Eric was unable to complete that number. During the encore break we were able to reset and the band finished as planned with the last number.
"The usual touring set length runs at one hour 35 minutes so in fact the full set was performed apart from the entirety of Cocaine which had to be curtailed."
Fans first realised something was wrong when Clapton walked off the stage part way through the song Cocaine. He returned after a few minutes and said "sorry about that" to the audience before playing the final song High Time We Went.
Although Clapton finished his full set list for the concert, excluding Cocaine, fans were left confused as to what had happened and many booed the seasoned performer. Others questioned why Clapton had not explained to the audience what was happening.
A spokesman for the SSE Hydro also apologised to fans and said: "The production team for last night's performance suffered a technical issue which resulted in the concert ending earlier than anticipated.
"By the time the venue had been made aware of the circumstances patrons were already leaving the bowl. However, our stewards and staff did their best to convey this information to customers as it became known."
One concert-goer, Wojtek Sromek, wrote on social media: "For a guy who travelled across half Europe to see Clapton at the SSE I feel truly unsatisfied. All in all, sorry to say, but it was quite a disappointing experience."
Lorna Macleod wrote: "Manners don't cost anything - perhaps Mr Clapton should remember that when his fans have paid £60 a ticket."
Others defended Clapton. Matt Bates wrote on HeraldScotland: "Yes, Eric walked off stage, but again, for the sake of accuracy, rather than sensationalist rubbish, he returned, apologised, and the band played the encore."