The home side took the lead moments before half-time as Ross Barkley and Leon Osman combined, with the latter's cross to the far post nodded back across goal by Nikica Jelavic for Naismith to head beyond Petr Cech from close range.
Chelsea had already missed a host of chances in the first period, with Samuel Eto'o unable to open his account on his debut for the Stamford Bridge side and Gareth Barry preventing a certain goal with one superb challenge on the former Cameroon international.
Jose Mourinho, who tastes defeat for the first time in his second spell at Chelsea, saw his side dominate proceedings after the break and push Everton back for long periods, but they were unable to find a way past Tim Howard and his superbly organised defence.
The much-anticipated Premier League debut of Eto'o did not go to plan for the 32-year-old, who was outshone by Barry making his first appearance for the Toffees after his deadline-day loan move from Manchester City.
His class is not in doubt but the former Barcelona and Inter Milan forward may be a bit rusty after a money-spinning spell in Russia with Anzhi Makhachkala.
It certainly looked that way when he headed wide Ramires' cross after five minutes when he should have - at the very least - hit the target.
More embarrassingly the striker then ballooned a long-range shot into the upper tier of the Gwladys Street end.
But Everton offered precious little up front themselves, with Jelavic's weak header and Naismith's cross-shot palmed away by Cech at the near post all they could muster in the opening half-hour as midfielder Barkley began brightly but faded quickly.
And Martinez's preference for them to play out from the back almost cost them a goal when goalkeeper Howard tried to pass square from his six-yard box.
He found only Andre Schurrle, who cut back for Eto'o to shoot into an open goal but as the striker eyed his first goal in English football, Barry slid in with perfect timing to deflect the ball behind.
The England international, out of favour at City, brings a wealth of experience greater and different to that of his fellow 32-year-old, midfield partner Leon Osman.
And it may have been his first outing with his new team-mates but Barry's positioning, reading of the game and general calmness under pressure gives the Toffees a first-rate shield in front of the back four.
Chelsea cranked up the pressure in the 15 minutes before the break with Howard saving Ramires' shot from an Eto'o pass, Schurrle firing over after Ramires' run and Branislav Ivanovic heading over Juan Mata's free-kick.
But with 30 seconds of one added minute remaining Osman crossed to the far post where Jelavic managed to keep the ball alive and Naismith, who had previously fired wastefully wide from Kevin Mirallas' shot, bundled home a header from close range.
Chelsea's tempo went up another notch after the interval and within 60 seconds of the restart Ramires played in Schurrle, who clipped over Howard but into the side-netting.
Martinez brought on £13million signing from Wigan, James McCarthy, to shore up the midfield at the expense of Jelavic with 25 minutes to go but Chelsea continued to threaten, with Ramires deflecting an Ivanovic cross into the side-netting.
Chelsea seemed to lose their way as Everton grew in confidence in the closing stages and David Luiz was booked for pulling down Mirallas as the Belgium international threatened to break clear on the halfway line.
Naismith departed to a standing ovation and took his seat in the dug-out to watch Leighton Baines clip the angle of post and crossbar with a 90th-minute free-kick.