Albion are facing a tense final fortnight of the season after throwing away the chance to virtually secure safety.
The Seagulls lost 2-1 at Wigan and have seen their lead over Millwall cut to six points.
Dale Stephens ended Albion's long wait for a goal with a 55th-minute equaliser.
But James Perch claimed the scrambled 81st-minute strike which kept Wigan's feint survival hopes alive.
Albion looked favourites to go on and win after Stephens volleyed in Danny Holla's corner.
Kazenga LuaLua shot wide with their best chance after Beram Kayal's clever touch sent him clear.
But poor defending by Greg Halford allowed Mac-Antoine Fortune to cross and Perch grab what had looked an unlikely winner.
The Latics went ahead on 26 minutes with a header by local boy Tim Chow on his full debut.
David Stockdale kept his side in the contest with a fine save in a one-on-one right on half-time.
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