Ex-Gunner Luis Boa Morte did his old club a favour with Fulham's equaliser to dent United's title challenge.
Title favourites Arsenal remain unbeaten in 27 Premiership games this season and last lost in the league in May 2003.
But the Gunners, so dominant in the first half, finished with nerves frayed. They hung on by the width of an upright after Claus Jensen gave Charlton a lifeline and substitute Jonatan Johansson came within inches of an equaliser.
Arsenal boss Arsene Wenger said: "We played great football early in the game.
"We played simple passing and quick movement and we always looked capable of scoring. But we needed a third goal to finish it completely. At 2-0 their goalkeeper (Dean Kiely) kept them in the game."The Gunners had won a gruelling Champions League match 3-2 at Celta Vigo on Tuesday and Wenger felt their energy levels dropped in the second half.
"We lost some sharpness and dropped physically as Charlton came more into the game," he added.
"We ended up edgy and nervous, a bit lucky even. I watched Johansson's shot rebound off the post and I thought we were fortunate that no Charlton player was there to put the ball away."FIFA president Sepp Blatter had said on Friday: "In my opinion, Arsenal are the best team in the world at the moment."They looked it in the opening stages with a breathtaking display of creative football. If their finishing had matched their approach work, they could have routed Charlton inside half-an-hour.
Charlton were the last London team to win at Highbury - 4-2 in November 2001 when Jensen scored. Wenger said: "I remember that game. We were punished for not taking our early chances." This time Arsenal started as if they would blow away Alan Curbishley's side.
In the second minute, Freddie Ljungberg cut in from the right and found Henry.
The Swede took Henry's return pass and crossed for Pires to sweep the ball home from close range. It was Pires's 50th goal for the Gunners.
Wenger said: "He has made a fantastic impact for us. He came here anonymous but he has become one of the club's greats. He makes a great contribution to our attacking play."Henry added the second, two minutes later. Patrick Vieira's pass dissected the Charlton defence, Henry controlled the ball on the run and smacked a shot past keeper Kiely.
Henry likes playing against Charlton. It was his ninth goal in seven games against them and his 20th in the Premiership this season.
Curbishley had picked five at the back. Jonathan Fortune, replacing the suspended Chris Perry, lined up with Mark Fish and Hermann Hrediarsson in the centre. Arsenal's flying start made his game plan redundant.
The leaders kept up the pressure. Luke Young blocked Ashley Cole's strike, Dennis Bergkamp shot too high, Edu curled a 25-yarder narrowly wide and Young blocked another Bergkamp effort.
Paolo di Canio managed Charlton's first attempt, a 19th-minute shot that failed to trouble Jens Lehmann.
Arsenal replied with another Edu strike. Ljungberg forced Kiely to tip over his rising drive and then the Charlton keeper held Vieira's shot.
Henry flicked the ball over a challenge, but shot straight at Kiely. Bergkamp fired over from distance again and Kiely did well to save from Henry after the striker's shot bounced awkwardly in front of him. Edu ended the first half with another free-kick past a post.
Charlton opened the second half with a more physical approach, typified by Hreidarsson's swift challenge on Ljungberg. They closed down Arsenal with renewed enthusiasm.
Jensen fired them back into the game after Lauren's 58th-minute foul on di Canio. The Dane, who scored the winner against Blackburn last Saturday, swerved the free-kick past Lehmann off the inside of an upright. Arsenal were stunned.
They continued to miss chances. Pires slid Henry through but Kiely saved low with his feet. Vieira nodded Bergkamp's free-kick wide from close range and Kiely turned round another Henry effort before the Frenchman clipped the bar with a cross-shot.
But Charlton posted a warning when Graham Stuart headed back across goal from Carlton Cole's centre.
In the 78th minute, Curbishley sent on striker Johansson for full-back Radostin Kishishev. Jensen fired over from 20 yards with five minutes left and then, in the dying seconds, Johansson hit a spectacular overhead kick past Lehmann - but the ball cannoned off a post.
Wenger said before the game: "Charlton have a stable squad, a stable manager and they're Premiership regulars now.
"That's why they're doing so well. If they were to gain a European place, that would be as good as some other clubs winning the championship."Charlton remain fifth, though Liverpool can overtake them if they beat Leeds on Sunday.
The Addicks missed the threat of Jason Euell, who had a knee injury. They lacked early bite in the wake of midfield powerhouse Scott Parker's move to Chelsea.
Curbishley will also be much happier when defenders Richard Rufus and Gary Rowett return from injury. But his team showed their spirit, and quality, by fighting back to give the leaders such a late fright.
Man of the match: Thierry Henry - Another performance of fluency and menace. Scored one goal and could have had a hat-trick but for Charlton keeper Kiely.