The five-star display ensured the Trotters gained sweet revenge for last season's FA Cup semi-final defeat by the same opponents.
Ivan Klasnic and Chris Eagles both struck twice as struggling Bolton secured a win that could kickstart their troubled season.
Captain Kevin Davies also got on the scoresheet for the hosts.
Stoke goalkeeper Asmir Begovic was at fault for both Bolton's opening goals but there was no doubting the superiority of the hosts after that.
The Potters were no doubt drained from Thursday's Europa League trip to Tel Aviv but Bolton were in no mood to spare them.
The Trotters' decline can perhaps be traced back to that 5-0 drubbing by Stoke at Wembley last April, after which they had lost 13 of 16 league games ahead of Sunday's encounter.
Manager Owen Coyle restored captain Kevin Davies to the side and handed a league debut to youngster Joe Riley as he sought a winning formula.
That it worked perhaps owed a little to fortune early on as Bolton controversially went ahead after two minutes.
First referee Howard Webb penalised Begovic for a back pass after Glenn Whelan lobbed the ball into his own area and Matthew Upson left it to the goalkeeper.
The Potters had barely had time to contest the decision before Klasnic grabbed the ball and a tapped a quick free-kick for Kevin Davies - recalled after being left out last week - to roll into an unguarded net.
Several Stoke players raced to protest to Webb but the official let the goal stand.
Bolton had another chance when Eagles shot from distance but Begovic parried and Andy Wilkinson cleared.
Stoke responded as Jermaine Pennant raced through and pulled back from the byline but Peter Crouch failed to make clean contact and Jussi Jaaskelainen saved.
Bolton came forward again and Begovic saved well from a powerful Mark Davies drive.
Bolton doubled their lead on 23 minutes after another horror moment for Begovic.
The keeper slid in to clear from the feet of advancing Klasnic but succeeded only in finding Eagles and the former Burnley midfielder brilliantly fired into the bottom corner from a tight angle.
Stoke took time to recover from the loss of the second goal and it was Bolton who dominated possession as half-time approached.
Pennant did make one penetrative run but Nigel Reo-Coker broke up the attack on the edge of the area.
Jon Walters won a header as Pennant launched a free-kick into the area in the last minute of the first half but Jaaskelainen batted out and Bolton scrambled clear.
Walters created a chance for Stoke after the break but Cameron Jerome glanced over from the Republic of Ireland international's cross.
Jonathan Woodgate made a timely interception as Reo-Coker aimed a dangerous cross towards Kevin Davies and Klasnic blasted a free-kick wide.
Stoke's next opportunity came from a typical Rory Delap throw-in as Robert Huth aimed a firm header at goal but Mark Davies headed off the line.
After that Bolton took complete control.
Huth was out of luck again as he headed a clearance straight at Eagles, who had regularly troubled him, and quickly fed Paul Robinson.
Robinson played the ball inside and Klasnic brilliantly swept home with a left-foot shot from the edge of the area.
Bolton's confidence was evident and they poured forward again with Mark Davies having a shot blocked and Reo-Coker firing the rebound straight at Begovic.
The fourth goal came in the 73rd minute and was deserved reward for the excellent Eagles.
Kevin Davies flicked a long ball into the path of Klasnic and the Croatian instantly touched on for Eagles to race through and slip the ball past Begovic.
Bolton then began to run Stoke ragged and grabbed a fifth nine minutes from time when Klasnic diverted a David Wheater header past Begovic.
Substitute Tuncay was then inches away from turning in a Riley cross for a sixth in the closing moments.