Despite being outplayed in the second half, Wigan could and probably should have stolen a point as Charles N'Zogbia hit the crossbar with the last kick of the game and was also denied a penalty.
Wigan were unable to battle back as Cahill scored his 21st headed goal in professional football late on and his sixth goal of the season to stop Martinez's men earning a point.
You just never know what you're going to get from Wigan Athletic and so it proved once again as Martinez's men produced a mixed display.
Despite outplaying Wigan in the opening 45 minutes Everton, and in particular Louis Saha, were left frustrated at the DW Stadium.
The injury-plagued French striker saw a deflected first-half shot hit the post, while Vladimir Stojkovic made a fantastic diving save to keep the scores level.
Everton should have scored early, but after Australia international Cahill appeared to handle the ball in the build-up, Leon Osman could only shoot straight at Stojkovic.
The miss of the first half though fell to Wigan striker Hugo Rodallega who, after racing clear on goal, fired straight at Everton goalkeeper Tim Howard.
Wigan striker Jason Scotland also had a couple of sights on goal, blazing over midway through the half before firing high over the bar just before the interval.
Everton started the second half the stronger, and Stojkovic had to be alert to parry away a free-kick from old-boy Leighton Baines.
Moments later Wigan were furious when N'Zogbia was tripped by Johnny Heitinga, with referee Lee Probert giving the free-kick an inch outside the area instead of pointing to the spot.
Everton were somehow denied a penalty in the final quarter when Marouane Fellaini was wrongly flagged offside after Osman and Cahill had created an opening.
But with six minutes remaining the Latics were not as lucky when Baines sent over an inviting cross for Cahill to head home.