The former Wolves defender rose highest to meet substitute Thomas Gravesen's corner and squeeze the ball past Mikel Alonso guarding the post.
It was cruel on Sammy Lee's team, now beaten four times in five Premier League games, but once again poor defending proved their undoing.
Indeed, Leon Osman might have claimed the winner himself just moments before Lescott's goal, but skied a shot into the ranks of the Everton supporters.
Until the late drama, Anelka showed just why his services were so coveted prior to the closure of the transfer window.
Bolton trailed to Yakubu's first goal since his big-money move from Middlesbrough, before their French talisman appeared to rescue a point.
Phil Jagielka and Joseph Yobo both tried to clear El-Hadji Diouf's cross and only helped the ball into Anelka's path.
With one mighty swipe of his right boot the former Liverpool, Arsenal and Real Madrid striker netted his fourth goal in five games.
Bolton fans joyfully sung Anelka's name before kick-off in recognition of his decision to commit his future to the club and they like him even more after another great strike.
However, despite bringing on new signing Andy O'Brien at half-time, Bolton are still leaking goals and until Lee rectifies the problem Anelka's goals will only be decoration.
Yakubu, one of three players making their first starts for Everton, didn't need long to start repaying his £11million transfer fee and all three newcomers were involved in the goal.
Jagielka dispossessed Anelka, deep in Everton's own half. Steven Pienaar, signed on a season-long loan from Borussia Dortmund, then played an exquisite pass that Gerald Cid tried in vain to reach before Andy Johnson.
That allowed Johnson a direct run on goal, allowing him time and space to provide the perfect assist for Yakubu.
Bolton hit back strongly and had justifiable penalty appeals turned down for Lee Carsley's clumsy attempted tackle on Diouf.
Tim Howard saved acrobatically from Alonso's arrowing long-range shot, while Diouf volleyed over after Kevin Nolan headed on Nicky Hunt's long throw.
And the action remained frantic and entertaining throughout the remainder of the half.
Alonso smacked an angled 25-yard drive off the crossbar while Jussi Jaaskelainen did well to keep out a Yobo header.