Demba Ba opened the scoring in the first half with his 15th league goal of the season before Yohan Cabaye made it 2-0 in the 47th from a free-kick. A Phil Jones own goal late on made sure Newcastle stayed seventh and a point behind Liverpool.
United's third defeat in 20 matches so far meant they stayed second on 45 points, only three ahead of third-placed Tottenham Hotspur who have a game in hand.
"It's not the time to panic. We've got the experience to cope with it," said United manager Sir Alex Ferguson, whose team lost 3-2 to Blackburn on New Year's Eve.
Howard's booming wind-assisted clearance bounced over opposite number Adam Bogdan and was only the fourth goal scored by a goalkeeper since the Premier League was formed in 1992/93.
Better was to follow, when two minutes into the second half Cabaye unleashed an unstoppable free-kick. Then, with United laying seige to Newcastle's goal, defender Danny Simpson stopped a Wayne Rooney shot on the line to keep the two-goal advantage.
United's miserable night was capped with added-time approaching when Jones took his eye off the ball following another huge kick by Krul and headed it onto his leg to wrong-foot Lindegaard.
"We've had such a great season so far without actually turning over one of the top teams. Today we had our best team out and it showed," Newcastle manager Alan Pardew told Sky Sports.
"They won theirs last night and we lost ours, advantage to them of course."
