United's furious players surrounded referee Mike Jones at the final whistle on Saturday after they had been denied two precious Premier League points.
TV replays showed Rio Ferdinand played the ball as he slid in on Hatem Ben Arfa after an hour, with the hosts leading through Javier Hernandez's sixth goal of the season.
But the far-side linesman decided otherwise, awarding the visitors a spot-kick from which Demba Ba scored.
Despite the dismissal of Jonas Gutierrez, United were unable to force home a winner, with Tim Krul producing a series of outstanding saves and Red Devils old-boy Danny Simpson producing a brilliant goal-line clearance to deny Hernandez, who had a goal disallowed for offside deep into injury time.
The result means Manchester City can go seven points clear if they win at Liverpool tomorrow.
When he replaced Chris Hughton as Newcastle boss midway through last season, Alan Pardew could not have received a more unenthusiastic welcome on Tyneside.
Sir Alex Ferguson felt Newcastle's 12th managerial appointment since the departure of his old friend Sir Bobby Robson might have been a smart move. And so it has proved.
Unbeaten until last week's trip to Manchester City, the Magpies have soared with an easy-on-the-eye approach that has even brought the best out of former United winger Gabriel Obertan.
The Frenchman was rarely effective on this ground wearing red. Here, he tormented and teased fellow countryman Patrice Evra, twice nipping past him despite having virtually no room to work with.
On the first occasion, the visitors should have gone in front.
Instead, Ryan Taylor got his six-yard volley all wrong and completely missed his kick.
Demba Ba also had a decent chance, striding on to Hatem Ben Arfa's astute chip but failing to get sufficient power to his first-time volley to threaten David de Gea.
It was enough to keep the visitors' hopes of registering their first Old Trafford win since 1972 alive, even if their hosts had the best opportunity.
Fabio supplied it. The young full-back curled over a glorious cross which Ryan Giggs touched towards the corner.
However, instead of extending a sequence that has seen the veteran Welshman score in every Premier League campaign so far, Tim Krul stretched out and pushed the ball away, just as Javier Hernandez was closing in.
Hernandez was the most dangerous member of a United attack that had been bolstered by the return of Wayne Rooney.
The Mexican also had a shot saved by Krul and drove another effort over, with Nani also off target with a curling strike from the corner of the penalty area.
When Newcastle were last level at the break at Old Trafford, they went on to lose by six and they could have conceded four within 10 minutes of the restart this time around.
Fabio flashed a shot wide after pushing the ball through Ryan Taylor's legs, Rooney's header sailed over and Young skimmed a shot wide from Patrice Evra's cross.
It was just as well for United that they had profited from some bad luck on Steven Taylor's part as he stuck out a leg to turn away a Wayne Rooney piledriver.
With Krul out of the game, having dived to save, Taylor succeeded only in hitting Hernandez, who knew nothing about it as the ball bobbled into an empty net.
As Newcastle were getting swept off their feet, it seemed they were destined for another defeat until they benefited from a massive slice of good fortune thanks to a staggering intervention from the far-side linesman.
When Ferdinand slid in on Ben Arfa, he conceded what he, and referee Mike Jones, thought was a corner.
The linesman, John Flynn, had other ideas and immediately signalled for a penalty.
Ferdinand could not believe it, and TV replays showed why as he clearly played the ball.
As the arguments raged, Demba Ba kept his cool and sent De Gea the wrong way.
United's players were clearly unhappy though, with Ferdinand, Rooney and Evra all making their feelings known as Newcastle celebrated their equaliser.
It was the moment that lit the blue touchpaper, with tackles flying in and every decision being contested as United raged at the injustice.
Gutierrez pushed his luck too far when he slid through the back of Nani. Having already been booked, the red card was virtually automatic.
From the free-kick, Krul brilliantly denied Nemanja Vidic as he turned away the Serbian's powerful header before denying Patrice Evra in equally acrobatic fashion.
Simpson then magnificently turned away Hernandez's goalbound header before United's final hope was extinguished thanks to an offside flag.