Scott Arfield's last-minute strike gave Burnley a famous Merseyside win double as Everton joined Liverpool in leaving Turf Moor empty handed.
With Everton eyeing a place in the top four , the Clarets produced a magnificent defensive performance to earn a repeat of the win they enjoyed over the Toffees in their first taste of the Premier League in 2009.
Sam Vokes scored his third goal of the season to give the Clarets a half time lead, following on from the goal he scored in August's 2-0 victory over Liverpool.
Yannick Bolasie equalised 13 minutes into the second half as Everton then began to lay siege to the Burnley goal.
But with Tom Heaton again in outstanding form and the Clarets' defence giving everything for their cause Burnley refused to buckle again.
And in the 90th-minute Sean Dyche's side secured another priceless three points thanks to a wonderfully executed volley from Arfield, whose first goal of the season could not have been better timed.
With Steven Defour and George Boyd missing through injury, Dyche gave wideman Michael Kightly a first league start of the season and re-called Arfield in central midfield as the Clarets looked to become only the second side to beat Everton in the Premier League this season.
But Burnley's re-shuffled side had barely had time to settle when they presented the first chance of the afternoon to the visitors.
A rare mix-up between Michael Keane and Ben Mee allowed Kevin Mirallas a sight of goal but the Belgium international was unable to beat Tom Heaton, who stood tall to block.
Heaton had a busy opening 20 minutes, saving from Romelu Lukaku and then from Ross Barkley as the England international, restored to Everton's starting line-up, cut in and aimed towards the far corner with his right foot.
But with the Clarets' back line, aided and abetted by Dean Marney in front of them, working tirelessly to stem the flow, Everton were largely kept at bay for the remainder of the first half.
And Burnley had chances of their own before Vokes broke the deadlock.
Kightly could have marked his return with an early goal but volleyed over following a Johann Gudmundsson corner.
Vokes also worked goalkeeper Maarten Stekelenburg with a long-range effort following the kind of composed build-up that brought the opening goal six minutes before half time.
Marney was again involved with a positive ball forward to Gudmundsson, whose superb first touch opened things up for Arfield to run at the Everton defence.
Ashley Williams got back to get a touch to Arfield's attempted shot but that wrong-footed Stekelenburg, who could only palm the ball into the path of the predatory Vokes to poke home his second goal in as many games.
Everton responded positively at the start of the second half as Barkley again forced Heaton to save low down to his right and Lukaku just failed to get on the end of a low cross from Mirallas.
But just as it looked as though Dyche's men may have again drawn the visitors' sting, they levelled with almost an hour gone.
Burnley lost possession in Everton's half with Idrissa Gueye springing a counter-attack which saw Lukaku ferry the ball into the path of Bolasie.
The winger has made a positive start to his Everton career after signing from Crystal Palace for £20m in August and claimed his first goal for the club as he drilled the ball across Heaton and into the far corner.
With the momentum behind Everton, only a superb interception from Keane prevented Lukaku from meeting a Seamus Coleman pass with the goal at his mercy.
And with 17 minutes to go Dyche made his first change, sending on James Tarkowksi in place of Kightly to help shore things up from a deep-lying midfield position.
It was increasingly becoming a rearguard action for the Clarets with Heaton having to tip over a dipping long range drive from Bolasie.
On-loan Liverpool defender Jon Flanagan was then sent into the fray in place of the battered and bruised Stephen Ward as Burnley dug deep.
Dyche's men simply refused to budge and got their reward in the 90th minute through Arfield's superb finish.
The impressive Gudmundsson was unlucky not to grab the glory with a 25-yard shot that thumped against the bar.
But when the ball dropped to Arfield, the Canada international showed superb technique to volley first-time past Stekelenburg to open his account for the season in style and turn the heartache felt in conceding last-gasp goals against Hull and Arsenal into elation.
Burnley: Heaton, Lowton, Keane, Mee, Ward (Flanagan 83), Gudmundsson, Marney, Hendrick, Kightly (Tarkowski 74), Arfield, Vokes (Bamford 89). Subs not used: Robinson, Darikwa, Long, O’Neill.
Everton: Stekelenburg, Coleman, Jagielka (Valencia 89), Williams, Oviedo, Gueye (Cleverley 83), Barry, Bolasie, Barkley, Mirallas (Deulofeu 76), Lukaku. Subs not used: Robles, Lennon, Holgate, Funes Mori.