Everton stared the game wanting to clock their first double this season after beating the Trotters 2-1 at the Reebok Stadium earlier this year, while Bolton were seeking their first back-to-back wins since April after Saturday's 3-0 demolition of fellow strugglers, Birmingham City.
After celebrating the life of former Everton keeper Jimmy O'Neill with a standing ovation, the fans at Goodison Park were treated to a less than rapturous start to the game with both sides failing to get any real leverage into the match.
Bolton were defending comfortably deep, seemingly happy to feed Nicolas Anelka and Andy O'Brien on scraps and lost causes, while Everton's attacking threat was almost non-existent.
When the first shot of the game did come, Steven Pienaar ran almost the length of the field to feed an over lapping Joleon Lescott, who crossed the ball out to Mikel Arteta who saw his shot deflected out for a corner off Danny Guthrie.
Everton picked up after that and started to exert pressure by pinning Bolton back into their own half and warming the home crowd up with some neat interplay between Arteta, Cahill and Yakubu. The home team had three good opportunities from set-pieces as Bolton's challenges became slightly reckless, but failed to capitalise.
Bolton could have gone ahead in the 35th minute as Tim Howard flapped at Ivan Campo's cross, but Anelka couldn't turn to shoot before it was taken off his toes.
But Everton were unarguably the better team over the first 45 and finished the half strongly, actually putting the ball in the net, but Cahill was offside when Yakubu shot home after good work by Lescott.
Jussi Jaaskelainen was the hero in the opening seconds of the second half after saving point blank from Cahill after Yakubu's trickery had opened up a gilt-edged opportunity for the Australian international. Lescott should have scored also from the resulting corner, but his effort trickled wide.
Everton were turning the screw though with Arteta, Lescott and Thomas Gravesen going close and it was no surprise when they went ahead.
Phil Neville claimed the second goal of his Everton career with a little help from team-mate, Tim Cahill who jumped with Jaaskelainen to meet Neville's cross, sufficiently distracting the Bolton keeper to allow the ball to sail into the net.
Everton dominated after the goal with Arteta and Pienaar mesmerising the visiting defence with their footwork. At the other end, Anelka was completely contained by Phil Jagielka who is turning into the defender David Moyes hoped when he splashed £4million out on the former Sheffield United utility man in the summer.
Lescott did clear off the line in the 67th minute to maintain Everton's lead and the home side sealed it minutes later as Cahill swept home a Lescott cross, after referee Rob Styles allowed the advantage after Gravesen had been felled outside the penalty area and Pienaar had collected the loose ball.
In truth, after a dominant second half by the home side, Bolton were fortunate to leave the field beaten by just two goals.