The Latics forward, on his first Premier League start, caused outrage with a reckless knee-high challenge on substitute Massadio Haidara.
He escaped punishment but referee Mark Halsey sent off furious Newcastle assistant manager John Carver - who twice had to be restrained as he tried to confront McManaman at the end of the first half - and Wigan coach Graham Barrow in an unseemly fracas.
Jean Beasejour's first-half goal had been cancelled by Davide Santon with 18 minutes to go only for Kone to snatch a vital close-range goal in a goalmouth scramble in which the ball appeared to come off team-mate Maynor Figueroa's hand.
Substitute keeper Lee Camp ensured 10-man Norwich left Sunderland with a 1-1 on a day when the Canaries' luck deserted them.
Chris Hughton's men were leading 1-0 at the Stadium of Light through Wes Hoolahan's close-range header when keeper Mark Bunn was dismissed for handling outside his area, and their fortunes took a further turn for the worse five minutes before the break when defender Sebastien Bassong conceded a penalty.
Craig Gardner levelled from the spot and then forced a vital 59th-minute save from Camp as the Black Cats strove in vain for the goal they needed to secure a first win in seven Barclays Premier League games.
However, Norwich left Wearside believing they should have been awarded a 70th-minute penalty for handball against Danny Rose in an eventful encounter.
Frank Lampard scored his 200th Chelsea goal as the Blues climbed to third in the Barclays Premier League with a 2-0 victory over his old club West Ham in the London derby at Stamford Bridge.
On his 595th Chelsea appearance, Lampard headed in an Eden Hazard cross after 19 minutes to move within two of Bobby Tambling's club scoring record of 202 goals.
Former West Ham striker Demba Ba should have scored three times in the first half, but Chelsea went two goals ahead when the impressive Hazard netted after 50 minutes.
Victory took Rafael Benitez's side above Tottenham, who were beaten 1-0 by Fulham earlier on Sunday.
At White Hart Lane, Dimitar Berbatov came back to haunt his former club as Tottenham's chances of Champions League qualification took a huge blow.
Having scored three goals in his last four matches, Berbatov was always going to be Fulham's main goal threat, but even he could not have imagined how easy it would be to score his first goal at White Hart Lane since leaving Spurs in 2008.
The Bulgarian, who scored 46 goals in two seasons at Tottenham, easily spun off his marker and his mis-timed shot flew past Hugo Lloris to give the Cottagers their first win at White Hart Lane in 10 years.
The win must have proved even more sweet for Martin Jol, who tasted victory at Spurs for the first time since he was harshly sacked in 2007 after two top-five finishes.
Andre Villas-Boas' side have now lost three successive games for the first time under his stewardship and they sit four points above Arsenal having played one more game.
1 Man Utd 74 2 Man City 59 3 Chelsea 55 4 Tottenham 54 5 Arsenal 50 6 Everton 48 7 Liverpool 45 8 West Brom 44 9 Swansea 40 10 Fulham 36 11 Stoke City 34 12 Norwich 34 13 Newcastle 33 14 West Ham 33 15 Sunderland 31 16 Southampton 31 17 A Villa 30 18 Wigan 27 19 Reading 23 20 QPR 23
Source: Newcastle United Mad