The rockers were added to the first-day line-up at the last minute after Florence + the MAChine were bumped up to headliners when Foo Fighters pulled the plug on their set to allow frontman Dave Grohl to recover from a broken leg he sustained during a recent show in Sweden.
The group's triumphant set began with versions of fan favourites The Delaney and Vertigo, and Doherty took a moment before the band played Time For Heroes to honour his late friend.
He said, "Alan Wass, if you're up there looking down, or down there looking up..."
Wass died after suffering a heart attack earlier this year (15).
The Libertines weren't the only day one 'surprise' for Glastonbury revellers - The Charlatans and Bastille also performed low-key sets.