Wigan had Lee McCulloch sent off but they celebrated Paul Jewell's manager of the month award with their fifth Premiership win.
And the early kick-off meant they got to sample the dizzy heights of second spot in the table, at least temporarily.
Powerhouse striker Jason Roberts got the winner to pile the pressure on Graeme Souness but the Magpies were twice on the receiving end of controversial decisions in the second half.
Referee Phil Dowd turned down a penalty appeal and his assistant Andy Williams insisted that a header from Alan Shearer had not crossed the line before it was cleared by Leighton Baines.
Wigan were unchanged with all seven of their internationals returning from World Cup duty injury free.
Newcastle had England hero Michael Owen back with Turkish star Emre returning on the bench after injury.
But the Magpies were still missing key players including Kieron Dyer, Albert Luque, Celestine Babayaro and Nobby Solano as they attempted to improve on their two-win start to the season.
It was the first meeting between the two clubs since way back in 1954 when non-league Wigan - then in the Lancashire Combination - were beaten in an FA Cup replay at their old Springfield Park ground in front of a 26,000 crowd.
Moe than half a century on, it was another near sell out, this time at the JJB stadium, and Wigan had the chance to stretch their unbeaten Premiership run to six games.
And they made an encouraging start with man of the match Roberts carving out two early chances.
The first was all about instinct after a left-wing cross from Baines was only half-cleared by Robbie Elliott and fell straight into Roberts' path. He reacted instantly with a terrific volley but it flashed just past Shay Given's right hand post.
The big striker's next effort was all about speed and strength - and a touch of bad luck.
A Baines ball skidded off the head of Jean-Alain Boumsong and Roberts took advantage. He had the strength to hold off Steven Taylor before having a crack at goal, but the left foot shot struck the outside of the post.
United had a clear chance after 26 minutes when Lee Bowyer should have cashed in on an uncharacteristic slip by experienced centre-back Stephane Henchoz.
Goalkeeper John Filan was out of position and in trouble when Bowyer fired in a tame shot which came back off the post, allowing Filan to recover.
Owen put another over the bar from an Amady Faye cross having earlier struggled to unlock the Wigan defence.
Newcastle were dangerous on the break and Wigan were almost caught out when Owen played Charles N'Zogbia free on the left. The French teenager hammered in a shot, forcing Filan to dive to his left to save.
Visiting keeper Given almost died of embarrassment when a long ball from the back bounced over his head, and he had to beat a hasty retreat to prevent further damage.
But he was beaten in the 40th minute when Wigan took the lead.
Henri Camara and Damien Francis provided the assist and although Given managed to get a touch to the shot from Roberts, he could not prevent it from crossing the line with his defence slow to react.
Wigan went close again from a well worked free-kick when Jimmy Bullard - making a club record equalling 117th consecutive appearance - hit a swerving shot just over the bar.
United boss Graeme Souness was clearly aggrieved when Shola Ameobi was denied a penalty after being clipped by Filan, and his protests earned him a touchline lecture from referee Dowd.
There was more controversy when Shearer's header from an Emre corner appeared to cross the line. But the officials gave the benefit of the doubt to Wigan defender Baines who hacked the ball clear at the back post.
Five minutes from time Wigan were reduced to 10 men when Lee McCulloch sent off for a bad challenge on Emre, but the Latics managed to hang on.
They even almost snatched a second in stoppage-time when Stephen Carr raced back to block a strike from substitute David Connolly after a Wigan breakaway.
Man of the Match: Jason Roberts
A powerhouse performance from the big man, who proved a constant danger and was unfortunate to finish with just one goal.