In a tough encounter, which saw a red card for John Obi Mikel and six other yellow cards, Shaun Wright-Phillips scored in the first half before Yakubu netted an equaliser for the visitors just past the hour mark.
A spiky opening with tough challenges by both sides saw Lee Carsley get a yellow card for dissent on nine minutes.
Good approach play by the home side saw Juliano Belletti blast an opportunistic 30-yarder high and wide over Tim Howard's crossbar on 12 minutes.
But the breakthrough for Chelsea came on 25 minutes when a simple throw-in by Wayne Bridge fed Florent Malouda. The French winger passed an accurate ball to Wright-Phillips who had ghosted to the edge of the Everton area.
The England winger curled an inch-perfect shot around centre-back Joseph Yobo and past the despairing dive of Howard and the ball zipped off his left post and into the net.
Michael Ballack almost doubled the lead two minutes later when his blistering free-kick from just outside the area arrowed agonizingly wide of the Everton goal.
The visitors' first worthwhile effort on goal came on 36 minutes when a cross-cum shot by Lescott, wide on the left, fell comfortably into the arms of Hilario.
Wright-Phillips almost scored a minute into the second half. This time his right-footed shot from the edge of the area was weak and easily held by Howard.
Chelsea were reduced to ten men on 55 minutes when a lunging one-footed challenge by Mikel on Neville saw a red card brandished by referee Peter Walton.
Pizarro's limp shot on 59 minutes should have extended Chelsea's lead, but it was all too easy for Howard to smother the shot.
Steve Sidwell replaced Joe Cole to bolster the midfield on 60 minutes. But it did no good as Everton equalised on 63 minutes when, following James McFadden's left-sided free-kick, Hilario completely missed the flight of the ball and the ball fell invitingly to Yakubu, who blasted the ball high into Chelsea's net from 12 yards out.
Everton deserved to get number two when James McFadden hit the base of Hilario's left upright on 68 minutes following a brilliant mazy run, wide on the left which cut through Chelsea's rearguard.
Avram Grant replaced striker Pizarro with full-back Paulo Ferreira with eight minutes remaining.
But it was pint-sized Wright-Phillips who forced Lescott into a late error and the ball bounced off the left-back and into the net to give Chelsea a 2-1 victory.