Roberto Martinez's side secure a vital win in their quest for Premier League survival but the game is overshadowed by Callum McManaman's horror challenge on Massadio Haidara
Jean Beausejour gave the Latics the lead in the 17th minute when he fired home from close range, but the home side should have been down to 10-men when Callum McManaman put in a horrendous challenge on Massadio Haidara, only to escape punishment.
Newcastle pressed after the break and finally got their leveller when Davide Santon powered the ball into the net from a tight angle. The game looked to be heading for a draw but the Ivorian popped up in the right place to turn the ball in at the death.
Roberto Martinez kept the same team that beat Everton in the quarter-finals of the FA Cup last Saturday as keeper Joel Robles started ahead of Ali Al-Habsi between the sticks.
Newcastle made three changes to their side that beat Anzhi Makhachkala on Thursday. Yoann Gouffran, Mathieu Debuchy and Sylvain Marveaux all returned to the line-up, while Yohan Cabaye missed out through injury.
Wigan began the game strongly and took the lead through Beausejour. McManaman picked up the ball and raced past Haidara and lifted a wonderful cross to the back post. The Chilean was free and made no mistake firing through the legs of Rob Elliot and past the despairing Steven Taylor.
McManaman was lucky to stay on the pitch moments later when he went in hard and high on Haidara, who had only just come on to replace the injured Debuchy. The youngster made no contact with the ball and he clattered studs first into the full-back's knee. Referee Mark Halsey, however, did not see the incident and McManaman went unpunished.
Martinez’s side almost doubled their lead when Shaun Maloney was denied by Elliot. The Scot turned his man on the edge of the area and fired a dipping shot towards the bottom corner but the keeper was there to make the stop.
Newcastle could have grabbed an equaliser late in the half as the ball fell kindly to Papiss Cisse in the penalty area but he could only direct the ball over the bar as he and James Perch got in each other's way.
As the half-time whistle blew an altercation erupted between McManaman and Newcaste assistant John Carver near the players' tunnel. Stewards grappled with the Magpies man to curtail the brawl. As a result, Carver was sent to the stands along with Wigan coach Graham Barrett.
McManaman nearly got his side's second goal shortly after the break, which would have undoubtedly sparked further outrage on the sidelines, but his goalbound shot was well blocked by defender Mapou Yanga-Mbiwa and the Magpies scrambled away the loose ball.
Newcastle were struggling to create many openings but Cisse should have done a lot better when he was put in behind the Wigan defence by Gouffran. The striker blazed his shot over the bar when he had players free in the area.
Cisse was to make up for that error as he played delightful ball to Santon to score the equaliser. The Italian raced on to the ball and drilled a low shot past Joel into the bottom corner with great composure.
The Magpies made a late press to win the game but it was Wigan who scored the decisive goal following a goalmouth scramble, leaving Kone to turn the ball into the net from close range and seal the win for the Latics. Newcastle were left fuming again, however, as replays showed a clear handball in the build-up to the winner.