The much-maligned forward, a surprise starter, nodded home from two yards after Nikica Jelavic had nodded back Leon Osman’s centre.
It was the visitors who started the game the stronger, debutant Samuel Eto’o sending a flashing header just over from Ramires’ centre on five minutes.
Naismith then broke clear down the right and put in a chipped cross for Jelavic, but he couldn’t get enough power on the header and Petr Cech saved.
Chelsea then began to assert themselves on the game and pinned Everton back, but the closest they came to scoring stemmed from a horrific Everton mistake just before the half hour.
Sylvain Distin and Tim Howard got themselves in a mix-up, with the American gifting the ball to Andre Schurrle, whose low pass set up an open goal for Eto’o, only for Gareth Barry to put in a superb last ditch tackle and send the ball out for a corner.
With Everton rocking, Howard made amends for his earlier error with a fine save to palm away Ramires’ goal-bound effort on 35 minutes.
At this stage Everton would have been grateful for the half time whistle, with Chelsea well on top, but they hit the Londoners with a sucker punch seconds before the break.
Ross Barkley fed Osman on the right hand side of the penalty area and he sent in a hanging cross that looked to be drifting out of play, only for Jelavic to stretch and nod the ball back to Naismith, who headed home from two yards beyond a stranded Cech.
Chelsea, no doubt stung by that late goal, came out after the break determined to get back in the game and nearly equalised in the opening minute.
Ramires found Schurrle in the box, but his chipped finish from a tight angle went into the side netting.
Three minutes later Eden Hazard stung Howard’s palms with a long-range drive and Eto’o failed to capitalise on the rebound.
Oscar was immediately in the action as he tried to burst in the area, colliding with Distin and Osman and going down claiming the spot kick, waved away by referee Howard Webb.
Branislav Ivanovic then broke free down the right and his cross found a stretching Ramires, but the ball went into the side netting.
Fernando Torres was predictably booed when he came off the bench but his arrival signalled a change in the game as Everton began to fight back.
First, Mirallas bent a free kick around the wall that drew a smart stop by Cech before the Belgian saw another effort parried away from a tight angle.
Chelsea at this stage were becoming increasingly ragged as they pushed for an equaliser, with Everton having the best chance in the final stages, Leighton Baines curling a free kick onto the top of the crossbar with two minutes left.
Everton held on through four minutes of stoppage time to claim a memorable first victory of the season in front of a jubilant Goodison crowd and really kick start their season.
It is always hard to pick out a man of the match after such a victory, with honourable mentions going to Naismith, Mirallas and Barkley.
However, my pick is Gareth Barry, who slotted into the team seamlessly and was the bedrock of this hard earned win. He could well be an astute signing by Roberto Martinez.
Howard 7 Baines 7 Jagielka 7 Distin 7 Coleman 7 Mirallas 7 (Deulofeu - 90' 6 ) Naismith 8 (Stones - 89' 6 ) BARRY 9 Barkley 8 Osman 7 Jelavic 7 (McCarthy - 66' 7)