Featuring four-time headliners Coldplay, as well as a slew of other acts such as Haim, Damon Albarn, Wolf Alice, Jorja Smith, George Ezra and Kano, technical issues with the live-stream were apparent from the beginning.
People who had paid the £20 ($28) fee to access a broadcast of the event took to Twitter to say that their access codes were invalid.
The problems persisted for two hours, after which organisers decided to launch a free live stream instead, meaning anyone could tune in, whether they had paid or not.
"I am so sorry about the problems with the stream tonight," said festival organiser Emily Eavis before offering a link to a new stream.
The replacement live-stream could only be rewound by an hour, meaning the early parts of the five-hour show were still unavailable.
To compensate, Eavis said: "We will obviously make sure we show the whole film again from tomorrow, too, and give you the chance to catch up on any bits you missed.
"I really hope you can enjoy the rest of it tonight. And again, I'm just so sorry to anyone who's had issues."
As complaints flooded in, Driift Live, partners of Glastonbury who organised the live stream, also said they were "devastated" by the technical issues experienced by paying customers.
Ticketholders who could not access the show will be offered a refund upon request.
Earlier in the night, Coldplay billed the concert as a "very special night at Worthy Farm tonight and a home gig for us", after headlining the Glastonbury in 2002, 2005, 2011 and 2016.
One of the other highlights from the show included Radiohead side project The Smile making its debut. Consisting of Thom Yorke and Jonny Greenwood, with drummer Tom Skinner, the trio joined the show between sets from Smith and Kano.
All the performers for the event waived their fees, with proceeds intended to secure the festival's future after being forced to cancel again because of the pandemic. However, now organisers will undoubtedly have to deal with thousands of demands for refunds.
In April, Glastonbury received a £900,000 grant from the UK government to help carry it through to 2022.
"This grant will make a huge difference in helping to secure our future," founder Michael Eavis and daughter Emily said.