The concert was to be the first in a series of summer events at the new venue, but nearly two hours into his set, the singer told the audience that he had been told to stop playing on police advice.
According to The Guardian, John told the crowd of almost 11,000: "I have been told there is some really bad weather on the way. The police say you need to leave right now in an orderly fashion.
"I'm sorry but I don't want anyone to be hurt. I'll make it up to you."
Earlier in the evening, the star had played hits such as ' Candle in the Wind', 'Rocket Man' and 'Sacrifice', and even joked with the crowd about the day's weather.
"I can't see anyone with a bikini on out there," he shouted, during what was his first show in the Lancashire city since 1977.
The venue, which lies in the shadow of Blackpool's famous tower, is due to host the Olympic flame and performances by The Wanted, McFly and John Barrowman in the coming weeks.
John is currently undertaking a world tour after performing during the Queen's Diamond Jubilee celebrations.
Pnau recently revealed the second single from their 'Elton vs Pnau' project, titled 'Sad'. The song - released on July 16 - includes elements from John's 'Nice and Slow', 'Sorry Seems to be the Hardest Word', 'Friends', 'Curtains' and 'Crazy Water'.
Watch the video for Elton John's classic hit 'I'm Still Standing' below: