Andre Gray continued his recent scoring spree and Josh Ginnelly grabbed a late winner as the Clarets maintained their unbeaten pre-season run.
Striker Gray, who terrorised Wanderers five months ago in the Clarets push for promotion, continued his 100% record in pre-season, making it five goals in four games with an early penalty, won through a combination of pace and trickery.
Jay Spearing replied with a fierce effort for Wanderers, who are putting the finishing touches to their own pre-season.
And following increasing second half pressure, the Premier League new boys won it as former Shrewsbury Town winger Ginnelly found the bottom corner with unerring accuracy after the chance looked to have gone.
The Clarets were without strikers Ashley Barnes and Lukas Jutkiewicz, who both suffered hamstring tweaks at Morecambe at the weekend.
David Jones also missed out through illness, along with Fredrik Ulvestad.
That meant a first senior start for striker Dan Agyei, alongside Gray in attack.
And the two combined well early on as Burnley started well, with Agyei’s intended cross to his strike partner headed behind for a corner.
And in the 16th minute, the Clarets went ahead with a goal of Gray’s own making.
Bolton defender David Wheater would still have been having nightmares about Gray’s brilliant brace here in the crucial win last season.
And when Gray turned the Trotters defender inside out, a hanging leg caught the Clarets striker, who dusted himself down to rifle home the resulting penalty.
Heaton had been untroubled, but 20 minutes from half time he was seriously tested by Spearing.
The former Liverpool man audaciously went for the top corner with a wicked free kick from the edge of the box, but the Clarets’ last line of defence expertly got a touch to divert the ball onto the top of the crossbar.
But Gray continued to cause Wheater problems and when he again showed his pace and weaved past the centre back, keeper Ben Amos saved the day with an outstretched leg.
Ben Mee was introduced at the break, along with Chris Long.
New signing Johann Berg Gudmundsson
And the Clarets defender’s intercepted pass led to the equaliser three minutes after the restart, as Spearing fired home from the edge of the area as the Clarets defence backtracked.
James Tarkowski headed over a Michael Kightly free kick and sub George Boyd fired straight at Amos as Burnley looked to regain the ascendancy.
And with 17-year-old Aiden O’Neill, the only outfield player to play the 90 minutes, pulling strings in midfield, Burnley continued to dominate the chances.
Chris Long was next to test the Trotters keeper after advancing from midfield and letting fly from 18 yards.
And the former Everton striker could have won it late on; forcing a fine, instinctive save from Mark Howard following a smart turn and shot.
It was left to Paul Robinson to preserve the status quo, diving low to his left to claw away Max Clayton’s low, angled drive.
But Ginnelly had the last word, refusing to give up after a late tackle from Alex Finney denied him and pouncing on the loose ball to fire home his first goal for the club and win it.
Burnley: Heaton (Robinson 66); Lowton (Darikwa 72), Keane (Mee 46) Tarkowski (K Long 72), Ward (Lafferty 66); Kightly (Ginnelly 81), Marney (Boyd 58), O'Neill, Arfield (Jackson 81); Gray (C Long 46), Agyei (Hennings 66).
Sub not used: Pope