It took the home outfit some time to play their way into the fixture, but when they did, they went in front. Callum McManaman's cross from the right was not cleared by the Newcastle defence and Jean Beausejour took full advantage by scoring his first goal for the club with 19 minutes on the clock.
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The remainder of the half was then overshadowed by an injury suffered by Massadio Haidara, who was stretchered off following a challenge with McManaman. Replays showed that the Wigan winger had caught the Newcastle defender late, but referee Mark Halsey didn't even award a free kick.
Visiting Newcastle provided more of a threat after the restart and they looked to have secured a share of the spoils when Davide Santon struck 19 minutes from time. The Italian full-back found himself with time and space on the right side of the penalty area and he struck a low shot beyond Joel.
© AP Photos
However, with the match approaching stoppage time, Wigan claimed all three points in controversial circumstances. Maynor Figueroa appeared to handle the ball in a goalmouth scramble but play was allowed to continue, and Kone fired in from six yards out.
While they remain in the bottom three, Wigan are now just three points from safety.