Wanderers were just seconds away from inflicting Everton's second defeat in their last 18 home games at Goodison Park, only to be denied in stoppage time following Jermaine Beckford's late leveller.
Ivan Klasnic had capped a superb flowing counter attack arriving at the back post to convert Matt Taylor's cross from the left wing, as the hosts ended the game with ten men following the dismissal of Marouane Fellaini for a kick out at Paul Robinson.
But Wanderers were denied right at the death, as substitute Beckford superbly bent a right-footed effort into the net from an acute angle.
Manager Owen Coyle named the exact same squad that dismantled Harry Redknapp's Tottenham Hotspur side last weekend at the Reebok Stadium, with Taylor maintaining his place down the left flank.
Although Coyle didn't enjoy his first trip to Goodison Park as Wanderers Manager last term, with the side losing 2-0, it is a ground where he had previously tasted success at as a player. Coyle played and scored in a 3-2 victory for the Trotters in a FA Cup tie between the two sides back in 1994.
And right from the off Stuart Holden showed just why he has earned the tag as the Barclays Premier League's top tackler in recent weeks, superbly timing two sliding tackles, the first a particularly important one on Steven Pienaar, who had made a dangerous into the Wanderers area.
Fellaini was back in the Everton side following a lengthy spell on the sidelines and his flick teed up Russian Diniyar Bilyaletdinov who skewed a left-foot shot wide.
But Wanderers weren't fazed by the early pressure from the home side, with Taylor and Chung-Yong Lee both enjoying a licence to roam from their respective wings.
Swede Johan Elmander, who has so far netted all five of his goals this term away from home, helped carve out the best chance in the early throes of the contest, latching onto a through ball only to be denied by a fantastic last ditch challenge from Sylvain Distin.
Wanderers had started the game positively, and even when the hosts enjoyed their fair share of possession, Wanderers slammed the door shut in the final third closing down their counterparts at every opportunity.
The Trotters enjoyed a spell of successive corner kicks on the 20 minute mark. Elmander continued to look the likeliest to find the net, narrowly heading wide from point blank range from Zat Knight's flick.
Everton carved out their first real chance of the contest on the 25-minute mark. South African Pienaar was the architect, threading a ball into Louis Saha's path before the Frenchman fizzed an effort straight into Jussi Jaaskelainen's frame, before the Wanderers stopper was alert to deny Bilyaletdinov's rebound.
Suddenly Everton created two clear-cut chances out of nothing. First, Chung-Yong hacked the ball off the line at the back post following a quick corner kick from the hosts before Jaaskelainen denied Saha from close range.
Fellaini was next to go close, as Wanderers' resistance was tested just before the break. The Belgian international lashed over from the angle of the six-yard box from a corner.
Wanderers were first to take to the field at the start of the second half and that reflected in the way the side started the second period. Elmander saw a rasping effort deflect narrowly wide of Howard's post before the American stopper pulled off a superb stop from the resulting corner denying Holden what would have been his first goal in a Bolton shirt.
It was positive stuff from Bolton, and Fabrice Muamba saw a tame effort easily held by Howard. But Everton fired a warning shot to Coyle's men, and on a rapid counter attack Gary Cahill narrowly diverted a low Leighton Baines cross over his own crossbar.
Skipper Kevin Davies, making his 300th appearance in a Bolton shirt, went close with a header from a corner as the tempo of game began ease. Coyle threw on Klasnic in place of Elmander in an attempt to mix things up in the final third.
Everton again enjoyed large spells of possession but failed to force Jaaskelainen into a save of note. In fact it was Wanderers who looked the more potent, as Taylor saw a glancing header from a corner clip the top of the crossbar with just 15 minutes remaining.
Everton were clearly frustrated and threw men forward in an attempt to break the Bolton resistance. But in doing they left themselves open at the back and Wanderers duly capitalised. Holden forced a mistake out of Phil Jagielka before releasing Taylor down the left side, who raced away before firing in an inch perfect ball across the face of goal for Klasnic to tap in at the far post.
It was Bolton's first goal at Goodison Park in four games and from the Croatian who had netted a winner against the Toffees at the death in the game between the two sides at the Reebok.
Everton's clear frustration was summed up in Fellaini's petulance, who having conceded possession to Paul Robinson, then kicked out at the Wanderers left-back before being shown a straight red card from the referee.
Just when it seemed the three points were secure after a thoroughly polished performance, Beckford popped up with the equaliser to cruelly deny Wanderers three points after Chung-Yong had unfortunately lost possession on the far touchline.
Everton: Howard, Neville (Yakubu 81), Jagielka, Distin, Baines, Bilyaletdinov (Coleman 66), Arteta, Fellaini, Pienaar, Cahill, Saha (Beckford 81)(Unused substitutes: Mucha, Hibbert, Rodwell, Baxter)
Wandereres: Jaaskelainen, Steinsson (Ricketts 59), Knight, Cahill, Robinson, Chung-Yong, Holden, Muamba, Taylor, Elmander (Klasnic 62), K Davies (Unused substitutes: Bogdan, Blake, Petrov, M Davies, Rodrigo)