The rockers gave fans just an hour's notice to their show in the the William Green tent, posting the news on Twitter.com.
Frontman Dan Smith wrote, "So happy to be back at Glastonbury! We play 13.30 at William's Green if anybody's about and fancies popping down.''
He opened the unannounced set by thanking festivalgoers for attending the show, stating, "Thank you so much for coming, it's amazing to be here. We've only got 40 minutes so we're going to play as much as we can for you.''
The group closed its set with the hits Of The Night and Pompeii.
Bastille weren't the only surprise early performers on day one of the festival - The Charlatans opened proceedings on the Other Stage.
Among the other first-day highlights so far was an appearance by Pussy Riot punks Nadezhda Tolokonnikova and Maria Alyokhina at Glastonbury's The Park Stage.
The Russian duo's set included an art performance and question-and-answer session hosted by singer and activist Charlotte Church, who called the punk pair "founding members of one of the most important and exciting movements that we've seen this century".
During the duo's performance spot, Tolokonnikova and Alyokhina climbed on a military vehicle to challenge an actor portraying a masked Russian soldier who declared, "We are not going to have any gay parades on this field."
The punks were arrested and jailed in 2012 for protesting in a Moscow church.