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.
Newcastle have already had problems with their touchline behaviour this season after manager Alan Pardew was banned for two matches for pushing assistant referee Peter Kirkup and more Football Association action is almost certain to follow.
The incident adversely affected the game as from the moment Haidara was carried off on a stretcher the mood changed significantly.
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.
Newcastle dominated the opening 15 minutes but had only Steven Taylor's header - saved by Joel Robles on his Premier League debut - to show for their efforts as a lack of pace to their attacks meant their hosts were rarely troubled.
By then Wigan's passing game had clicked into gear and within minutes from them establishing their rhythm they opened the scoring in the 18th minute.
McManaman crossed from the right and although Kone missed his header Santon failed to deal with the loose ball and Beasejour fired through the legs of goalkeeper Rob Elliot.
Unfortunately for him McManaman's next contribution brought him nothing but condemnation, although there appeared no malice or intent.
The youngster's over-zealous challenge did clip the ball but he followed through to smash into the kneecap of Haidara, who had only come on minutes earlier for hamstring victim Mathieu Debuchy.
McManaman escaped punishment from referee Halsey, who may have been unsighted, but as the defender departed in agony on a stretcher the atmosphere changed significantly as the game became much more niggly.
The only efforts of note in the remainder of the half saw Shaun Maloney's low effort tipped away by Elliot before Papiss Cisse volleys over from six yards after Paul Scharner inadvertently headed back towards his own goal.
Halsey's half-time whistle prompted a commotion on the touchline as Carver went for McManaman with Barrow also piling into the fray in defence of his player.
Both were sent to the stands for the second half but McManaman continued to be at the centre of everything as, just before his 58th-minute withdrawal, he had a chance to make it 2-0 but his shot was blocked by Mapou Yanga-Mbiwa.
By that time Haidara was already on his way back to hospital for the extent of his injury to be assessed as soon as possible.
McManaman's foul - and the subsequent fall-out - had undoubtedly affected the game but if anything it strengthened Newcastle's resolve - although their equaliser came from two uncharacteristic errors in possession from Wigan.
Shaun Maloney, on the right touchline, and then Scharner, even more crucially, gave the ball away and it was shifted from Cisse to Santon who fired home an angled shot.
Late on Cisse's close-range shot deflected wide by Robles was something else Halsey did not spot.
But just when it seemed a draw was inevitable Kone pounced in a goalmouth scramble from a corner, although Halsey's decision-making was again scrutinised as Figueroa appeared to handle in the build-up.
However, the victory was crucial for third-bottom Wigan, whose match in hand is at Manchester City, as both Aston Villa and Southampton won at the weekend.
Their survival, though, will not be the talking point with the immediate repercussions from the game likely to be discussed in the corridors of the FA.