Pop star Lily Allen stepped onto the main Pyramid Stage at 19:00 BST, 30 minutes later than planned.
Dance collective Rudimental had their set cut short as the storm approached.
Rudimental had just two songs left to play when the technical crew were seen running on stage and guiding group members out.
The crowd started to boo, unaware of the situation until another stage manager explained an electric storm meant it was not safe to continue.
The band were allowed to return to the stage to take a bow, but the electricity had been cut and they missed the last two songs from their set list, including the number one single Feel The Love.
A message on the large screens either side of the Pyramid Stage had read: “Thank you for your patience, we apologize for the inconvenience.
“In the interests of safety it was necessary to temporarily stop the show. Live music will return to the stage shortly.”
By 18:30 BST, the rain had eased off and the sky on the horizon had cleared.
Glastonbury organizers tweeted: “All stages are up and running after the short delay. Some set times are being adjusted slightly.”
Finally, power has been restored to the stages at Glastonbury.
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