Ten-men Bolton slipped to their second 2-0 defeat on Merseyside this season as goals from Mikael Arteta and Steven Pienaar secured Everton's seventh successive home win in the Premier League.
Wanderers defended manfully throughout but a key incident with 18 minutes remaining helped determine the outcome of the contest.
Gretar Steinsson was shown a straight red card - Bolton's third in the last four matches- for a professional foul and Arteta converted the resulting set-piece from outside the area.
And Pienaar completed the victory when he converted from ten yards out&nbsp;with just two minutes left.
Although Everton had the majority of possession in the second-half, Wanderers bossed the first 45 minutes and the game could have been different had Tamir Cohen or Kevin Davies managed to grab the crucial first goal before half-time.
Wanderers, who were unchanged from the victory over Wigan Athletic the previous weekend, had a penalty shout turned down by referee Alan Wiley within the first few minutes. A mini scramble inside the Everton box resulted in Johan Elmander prodding a shot at goal that appeared to strike the arm of John Heitinga, but the appeals for a spot-kick were waved away.
At the other end of the field, Paul Robinson made a superbly timed tackle on Victor Anichebe to prevent the young striker from getting a clear run on goal. If the left-back's interception had been a fraction late then it would have been likely that Robinson would have been sent for an early bath and the hosts would have had the opportunity to put themselves into the lead from 12 yards out.
Zat Knight forced Tim Howard into a close-range save after latching onto Chung-Yong's free-kick before Anichebe's afternoon came to an early end with just 15 minutes played as he was stretchered from the field with an apparent knee injury.
There was an unusually subdued atmosphere around Goodison Park in the opening exchanges as Wanderers managed to keep the home supporters quiet with an accomplished start.
Clear cut opportunities were at a premium although Phil Jagielka made a telling headed clearance, substitute Diniyar Bilyaletdinov thrashed a speculative left-foot effort way over the bar and Kevin Davies' 25-yard free-kick was well held by Howard.
Chung-Yong Lee's attacking qualities had certainly caught the eye throughout the duration of the 2009/10 season, but it was his defensive attributes that were most notable in the first-half.
Twice the South Korean made telling contributions inside his own penalty box - a headed clearance from Mikel Arteta's threatening set-piece and a stretched tackle on Leighton Baines as the left-back made dangerous run forward.
Nine minutes before the break, Tamir Cohen was a yard away from breaking the back of the net with a thunderous first-time effort from just inside the area and moments later, Davies almost completed a world-class passing move from the Whites.
Elmander, Chung-Yong and Wilshere cut the middle of Everton's defence apart with a sublime one-touch attack and it was only the heroics of Howard that prevented Wanderers from taking a half-time lead as he raced out of his goal to block the captain's attempt from eight yards out.
No changes were made by either manager at the break as Everton came out of the blocks the quickest. Wanderers had to be on their guard from the early pressure with Steinsson blocking a Pienaar shot and Jaaskelainen making a routine save to prevent Heitinga from finding the net with an attempt from outside the area.
Louis Saha was sent on by David Moyes with just over an hour played as the Everton boss looked to try and add some cutting edge to his team's play.
The Whites had defended resolutely but they were dealt a cruel blow when Gretar Steinsson was sent from the field with 18 minutes remaining and Everton took the lead with the resulting free-kick.
The Icelander had been deemed to have illegally denied a goalscoring opportunity when he brought down Yakubu just outside the penalty area and Alan Wiley had no hesitations in reaching for his red card.
Sam Ricketts was brought on as Owen Coyle looked to rearrange his team's formation, but only seconds later Mikael Arteta stepped up to bend the free-kick over the wall and into the corner of the net.
Knight almost equalised with a far post header and Coyle opted to introduce Matt Taylor and Mark Davies in the last ten minutes as Wanderers pressed for a means to get themselves back in the game.
Leon Osman wasted a glorious chance to double the lead when he was first to react to Jaaskelainen's parry from Heitinga's shot, however he could only strike the crossbar.
But on 88 minutes Everton did make it 2-0 as Osman turned provider, cutting the ball back for Pienaar, who put the game beyond Bolton.
With Jaaskelainen out of position, the South African international took the time to measure his shot before finding the back of the net from ten yards out to seal the win.
Bolton: Jaaskelainen, Robinson, O'Brien, Knight, Steinsson, Wilshere (Taylor 81), Cohen (Mark Davies 84), Muamba, Chung-Yong, Elmander (Ricketts 71), Kevin Davies (Subs: Cahill, Al Habsi, Riga, Weiss)
Everton: Howard, Baines, Heitinga, Jagielka, Arteta, Distin, Cahill (Saha 63), Neville, Pienaar, Yakubu (Osman 76), Anichebe (Bilyaletdinov 15) (Subs: Nash, Hibbert, Yobo, Rodwell)