Weekend camping tickets went quickly in just over an hour, before coach packages were snapped up by festival-goers.
The festival’s Twitter feed apologized to people who missed out after “demand far outstripped supply”.
The Rolling Stones, Mumford and Sons and Arctic Monkeys will headline the event in June at Worthy Farm.
Fans could reserve up to four tickets, which cost £205 ($320) plus a booking fee, when the site opened at 09:00 BST.
Glastonbury Festival organizer Emily Eavis tweeted asking for feedback on the ticketing process which has been criticized in the past for not being able to cope with demand.
Tickets for the event, which had a break last year to rest the fields, cost £10 ($16) more than the previous festival.
The Rolling Stones, who play on the Saturday night, will be performing at the festival for the first time.
Lead singer Mick Jagger said he would call U2 singer Bono for advice about their upcoming performance, following the Irish band’s 2011 headline slot.
More than 190 acts will appear at the event, including country star Kenny Rogers, Primal Scream, Nick Cave And The Bad Seeds and Elvis Costello.
New acts Rita Ora and Jake Bugg will appear on the main Pyramid Stage alongside Rufus Wainwright and festival veteran Billy Bragg.
Glastonbury Festival 2013 takes place from 28 to 30 June.
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