Leon Osman’s deflected strike and Phil Jagielka’s firm header put Everton in control, before Arouna Kone took advantage of a defensive mix-up to set up a nervy finish for the hosts.
With both teams struggling to adapt to the rainswept conditions at Goodison Park, the first-half was significant only for its lack of chances.
Wigan, who had replaced Franco Di Santo with Gary Caldwell to add defensive solidity, frustrated Everton and restricted their creative players from finding space in which to operate.
The visitors’ lone striker, Kone, threatened on the counter on a couple of occasions, but support was often slow to arrive to aid the Ivorian.
Everton became stronger as the half progressed, but they should have taken the lead as early as the 12th minute through Sylvain Distin.
But the Frenchman failed to make sufficient contact with Leighton Baines’ sweetly-struck corner from just a couple of yards out.
Towards the end of the first 45 minutes, Everton registered five corners in quick succession and, on the fifth one, Wigan goalkeeper Ali Al-Habsi’s punched clearance struck the arm of Shaun Maloney on its way out.
However, referee Lee Mason waved away Everton’s appeals for handball as the two sides went into the break goalless.
Everton started the second with the greater purpose and Thomas Hitzlsperger’s trademark long-range rocket clipped the top of Al-Habsi’s crossbar before flying behind.
Osman then attempted to dart through with the ball at his feet in the 50th minute, but his eventual stab at goal was smothered by Al-Habsi.
But the Everton midfielder would not be denied, as moments later, he opened the scoring with a strike which deflected off Caldwell’s arm and beyond the helpless Wigan goalkeeper.
With the hosts firmly on top, further chances came through Nikica Jelavic and Victor Anichebe but Everton’s strike duo were unable to add a quick second with Wigan reeling.
Maloney led claims for a Wigan penalty after claiming to be caught by Osman in the Everton box, but Mason remained unmoved.
That decision helped to ignite the visitors’ play, particularly Maloney, whose 65th minute cutback found Kone only for Phil Neville, making his 500th Premier League appearance, to stand firm to deny the Wigan striker.
But the visitors then struggled once more and, despite the introduction of Di Santo and Jordi Gomez, Everton seized the initiative and grabbed a second.
Neville expertly picked out Jagielka from the right, and the centre-back rose highest to firmly plant a 77th minute header beyond the outstretched Al-Habsi.
However, a defensive mix-up between Baines, Jagielka and Distin allowed Kone to slide in and cut Wigan’s arrears in half just five minutes later to unsettle the home crowd.
Roberto Martinez’s men failed to grab a late equaliser though, meaning Everton move up to fourth and into the UEFA Champions League qualification places, while Wigan remain rooted in the relegation zone.
MAN OF THE MATCH
Leon Osman (Everton) - Osman was at the heart of Everton's attacking presence, with his darting runs and close control causing the Wigan defence problem after problem. His goal was the icing on the cake following a committed display from the midfielder.
EVERTON: Howard 6, Neville 7, Jagielka 7, Distin 6, Baines 7, Osman 8, Hitzlsperger 6, Gibson 6, Pienaar 7, Jelavic 6, Anichebe 6. SUBS: Naismith 6, Oviedo 5, Heitinga 5
WIGAN: Al Habsi 5, Boyce 6, Caldwell 6, Figueroa 5, Stam 5, McCarthy 6, Jones 6, McArthur 6, Beausejour 6, Maloney 7, Kone 6. SUBS: Di Santo 6, Gomez 5.