Owen Coyle's side remain in the bottom three despite this victory but they are now only a single point from safety after two goals each from Chris Eagles and Ivan Klasnic and one from Kevin Davies secured their first home points of the season.
After losing eight of their last nine league games, and with memories of last season's 5-0 loss against Stoke at Wembley still painfully fresh, this was a cathartic moment for Bolton and Coyle, who will hope their biggest ever Premier League home win acts as a springboard to clamber out of trouble.
Stoke boss Tony Pulis was unhappy his side, who lost to Newcastle on Monday, were forced to play three games in six days this week and they were clearly lacking energy after a long trip back from Israel, where they defeated Maccabi Tel Aviv in the Europa League on Thursday.
Coyle had restored captain Davies to his starting line-up and handed a debut to 20-year-old Joe Riley as he made five changes in a bid to spark his struggling team into life.
The switches worked a treat and Bolton took the lead in controversial circumstances after just two minutes.
Referee Howard Webb penalised Asmir Begovic for picking up a back pass after Glenn Whelan lobbed the ball into his own area.
Stoke barely had time to regroup before Klasnic grabbed the ball and tapped a quick free-kick for Davies to roll into the empty net.
Several Stoke players raced to protest to Webb but the official was happy to let the goal stand.
Bolton had another chance when Chris Eagles tested Begovic from long range and the hosts doubled their lead on 23 minutes.
Begovic was at fault as he slid in to clear from Klasnic but slipped and could only hook his clearance to Eagles, who lashed into the unguarded net.
Jon Walters created a chance for Stoke early in the second half, but Cameron Jerome glanced over from the Republic of Ireland forward's cross.
Stoke went even closer when Robert Huth's header from a Rory Delap throw was nodded off the line by Mark Davies.
But Huth was out of luck again as Bolton bagged their third goal in the 61st minute.
The German defender's weak headed clearance allowed Paul Robinson to cross and Klasnic swept home with a left-foot shot from the edge of the area.
Bolton's fourth goal came in the 73rd minute. Kevin Davies flicked a long ball into the path of Klasnic and the Croatian touched on for Eagles to race through and slip the ball past Begovic.
Wanderers were in complete control and grabbed a fifth in the 81st minute as Klasnic diverted a David Wheater header past Begovic.
Source: AFP
Source: AFP