United, who led through Javier Hernandez's early second-half goal, were pegged back by Demba Ba's 64th minute spot-kick that left Sir Alex Ferguson's side four points behind City who play at Liverpool on Sunday.
"It was an absolutely shocking decision," a frustrated Ferguson told Sky Sports after defender Rio Ferdinand was harshly penalised for a tackle on Hatem Ben Arfa. "It cost us."
Tottenham Hotspur, with a double from Emmanuel Adebayor, stayed third after coming from behind to win 3-1 at West Bromwich Albion while Chelsea emerged from their recent slump to give under-pressure manager Andre Villas-Boas a huge boost with a 3-0 victory over Wolverhampton Wanderers at Stamford Bridge.
Arsenal moved up to sixth on 23 points despite being held to a 1-1 draw at home by Fulham.
Franco Di Santo struck a last-gasp winner to lift Wigan Athletic off the bottom with a 2-1 victory at Sunderland. Blackburn Rovers dropped to the basement after losing 3-1 at Stoke City in the lunchtime kick-off.
Manchester United have stumbled at home in this season's Champions League and after being held to a midweek draw by Benfica, they found high-flying Newcastle tough to crack on their return to domestic action, even when the visitors were reduced to 10 men after Jonas Gutierrez's 79th minute dismissal.
A fine performance from goalkeeper Tim Krul was overshadowed by Newcastle's equaliser.
Ferdinand appeared to win the ball fairly from Ben Arfa but assistant referee John Flynn signalled a penalty. Referee Mike Jones then awarded a spot-kick after consulting with his assistant and Ba slotted in his ninth league goal of the season.
"Everyone else, including the referee, was astounded. He was put in a terrible position... why can't the referee overrule the linesman when it is so clear to him and he was so near to him... he was only eight yards away. So that was one of the worst decisions I've ever seen," lamented Ferguson.
"The problem is the referees are full-time but the linesmen are not and whether he ever gets a game again, the assistant referee, is not for me to decide but it was an absolutely shocking decision."
United, who wasted a host of chances, were also denied by a late goal-line clearance and had a goal ruled out for offside in stoppage-time.
"In terms of creating chances we were fantastic today. If we play like that every week I'll be absolutely delighted," Ferguson added.
"Normally you would expect us to score three or four today with the chances we had... there was a bit of bad luck in terms of blocks on the line, their keeper has made two or three fantastic saves and we missed two or three glaring chances."
Chelsea, who had lost three of their previous four league games and their last two at home, cruised past Wolves after John Terry, Daniel St
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