Angry fans, who had to wait well into the early hours to see him, responded by chanting "Kanye sucks" and pelting the empty stage with glow sticks.
The delay was blamed on problems setting up a glow-in-the-dark backdrop for West's set
The four-day festival saw performances from over 150 acts, including The Raconteurs and comedian Chris Rock.
West had been due to perform at 0245 on Sunday morning (0745 GMT) but eventually took to the stage at 0425 (0925 GMT).
Many campers gave up waiting and returned to their sleeping bags.
Festival spokesman Ken Weins said the delay was caused by having to take apart Pearl Jam's set - after the band finished an hour late - and loading up Kanye West's equipment, which depicted him as a space traveller whose ship crash-lands.
West had originally been scheduled to appear at 2015 on Saturday evening, but he had specifically requested the late night slot.
Later on Sunday, pedal steel guitarist Robert Randolph criticised West on stage for disappointing his fans, inspiring more "Kanye sucks" chants.
Oh we would love to be there screaming "KANYE YOU SUCK!!!! EVERYTHING!!!"
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