It was a tough afternoon as the DW Stadium for Owen Coyle's men and just one goal settled it in a match defined by two opportunities just two minutes apart.
Andrew Crofts scored the vital goal on 72 minutes after a tremendous initial save by Lee Nicholls, but that moment came just after second half substitute Grant Holt had a clear cut chance to put his side ahead.
Latics remained unchanged from the 1-0 victory away at Yeovil Town before the international period.
The first 45 minutes saw Latics create the majority of the chances, but they were only half chances, other than an left footed effort inside the area from Nick Powell which was held well by Tomasz Kuszczak.
Marc Albrighton's width gave Latics a real threat, with his trickery and direct running style on offer, but the final finish couldn't be found.
A minute before half time his creativity found Marc-Antoine Fortune at the back of the penalty area, but after an initially well taken touch, the forward could only slide his shot into the side netting under pressure.
It was a similar story in the second half as Latics' wide threat created each chance.
Callum McManaman stung the gloves of Kuszczak from range, with the keeper spilling the effort but being aware enough to jump to his feet and pounce on the ball.
Latics made two changes within five minutes of each other on the hour mark, with Fortune replaced by Holt and Albrighton replaced by James McClean.
Grant Holt became the talking point of the game just 10 minutes after his introduction, when he muscled Gordon Greer off the ball from behind, allowing the forward to take a clear run on goal with just Polish stopper Kuszczak to beat.
Holt opened up his body as he looked to score the crucial opener for his side, but his effort was skewed wide not troubling the keeper and leaving the forward with his head in his hands.
The miss proved to be the moment that spurred Brighton on, and two minutes later Crofts had the ball in the back of the net.
Brighton attacked down the right hand side and a superb cross into the area found Craig Conway diving in at close range with a header.
Nicholls was quick to react, deflecting the ball away and up into the air, but his defence couldn't react quickly enough as Crofts pounced to loop a header back across the keeper and in at the back post.
It was a hammer blow for Latics who had quashed the advances of Brighton throughout the afternoon.
McClean led a spirited attempt to claim a point from the game as he seemed more determined than ever to help his side recover.
His cross created Latics' best chance to level when he found the head of Holt inside the area, but the striker saw his effort tipped out of the bottom right corner by the leaping Kuszczak.
Time ran out for Latics and the Seagulls flew away with all three points, taking advantage when they needed to.