The comic rougue Lee Nelson dashed on to the Pyramid stage and started dancing with the bemused rapper before being forcibly removed by security.
Kanye West's Glastonbury slot was the topic of hot debate even prior to the stage invasion.
The comedian ran on to the iconic stage during the fourth song with West trying to continue with the song, Black Skinhead, only to break off for security to remove him before restarting.
Lee Nelson, whose real name is Simon Brodki, also managed to sneak into a photograph with the England football team before last year’s World Cup in Brazil.
The headline slot drew tens of thousands to the Pyramid stage, having been one of the most controversial bookings in recent years. An online petition against West’s appearance garnered more than 100,000 signatories.
Television presenter Jonathan Ross was one of the stars watching the show from a viewing platform at the side of the stage, taking selfies with fans before the headline act began.
During Touch the Sky, Kanye walked off stage only to reappear being lifted high into the sky on a platform above the crowd.
He closed the lack-lustre set with the track All Falls Down from his debut album, before declaring: “You are now watching the greatest living rock star on the planet.”
Many festival goers left feeling dissappointed with the hyped Glastonbury set.