Leonardo Ulloa pulled a goal back for the Seagulls and Wigan soaked up heavy late pressure to clinch a 2-1 victory.
Brighton should have done better early on when Dale Stephens played the ball across the six-yard box and David Rodriguez was off target at the far post.
Wigan keeper Ali Al Habsi later went down to his right to save a goal-bound shot from Ulloa after David Lopez set up the opportunity.
The Latics had a let off when Stephens rose unchallenged and put a firm header just over following a perfect cross by Stephen Ward.
Brighton continued to move the ball well and, from a cross by Rodriguez, skipper Gordon Greer had an effort at the near post saved by keeper Al Habsi.
A mistake by former England international defender Matthew Upson led to Wigan breaking the deadlock on 21 minutes through McArthur, who burst through before beating keeper Tomasz Kuszczak with a well-placed left-foot shot.
The Seagulls came close to an immediate reply when midfielder Stephens saw his fierce shot come back off the underside crossbar after being set up by Ward.
Wigan had a good opportunity to extend their advantage when James McClean crossed accurately to the far post where Martyn Waghorn shot wastefully over.
Substitute James Perch, a half-time replacement for McClean, quickly made his presence felt and his low cross found Nicky Maynard whose deflected shot flew wide.
Midfielder McCann rose to increase Wigan's lead five minutes after the break, running across the penalty spot to head in an inswinging corner from Waghorn.
Brighton's Argentinian striker Ulloa, boasting three goals in his previous three games, put a header over from a corner by Andrea Orlandi.
Orlandi later drove a shot into the side netting before Rodriguez put a glancing header wide following a good delivery from compatriot Lopez.
Brighton, struggling to be clinical in front of goal, were wasteful again when Lopez shot wide after Ulloa helped on a cross from substitute Will Buckley.
The Seagulls, whose previous five wins in the Championship had all been by a 1-0 scoreline, sent on former Newcastle winger Kazenga LuaLua and Jonathan Obika in a bid to launch a late fight-back.
Ulloa reduced the deficit 12 minutes from time with his 10th goal of the season, firing in from close range after Upson headed back Orlandi's corner.
Brighton piled on late pressure and Al Habsi did well to parry an excellent ball in by Buckley before saving low down to deny Obika.