The Gunners completed the double over Manchester United to keep the Championship race alive, but the victory also cancelled out Chelsea's 2-0 loss to Liverpool to keep the champions within striking distance of the current Premiership leaders.
Arsenal had fallen behind to a rare Wayne Rooney headed goal on 53 minutes, but substitute Robin Van Persie levelled the scores on 83 minutes. As United appeared to be settling for a draw, up popped Henry to head the winning goal just moments before the final whistle sounded.
The game never really got going until the final minutes of the first half. Prior to that there were no clear cut chances apart from an effort when Henry headed into the grateful arms of Edwin Van der Sar on 34 minutes after Emmanuel Adebayor showed a good turn of pace to deliver a pin-point cross that deserved a goal.
As half-time approached the temperature in the Emirates Stadium began to rise, helped initially by a moment of controversy. The Gunners had a good claim for a penalty on 38 minutes when Henry cut into the right side of the penalty area and appeared to br felled by Gary Neville as the United captain put his leg across that of his Arsenal counterpart.
Referee Steve Bennett completely dismissed the home side's appeals, which the TV replays suggested had some substance.
Henry then hit a fiercely struck low shot, but, unfortunately for the Gunners his effort was straight at Van der Sar.
Manchester United then turned up the pressure demanding two world-class saves by Jens Lehmann in the third minute of first-half injury time.
Rooney picked up possession on the right side of the area and he let loose with a 25-yard dipping shot that Lehmann managed to just tip over the bar.
The resultant corning saw Henrik Larsson send a powerful header towards the bottom right corner, but the Gunners keeper got down quickly to his left to turn the ball around his post to safety.
The end of the first half promised much for the second and the beneficiaries were United. On 53 minutes Patrice Evra was allowed the time and space by Emmanuel Eboue to deliver a cross from the left which took a glance off the head of Kolo Toure.
That slightest of touches was enough to take the ball away from Lehmann and perfectly into the path of Rooney, who arrived late on the blind side of Gael Clichy on the right flank.
The England International claimed his first headed goal for United as he dived at the ball to nod it low into the bottom corner of the net beyond the Arsenal keeper's despairing dive.
It was also Rooney's first goal in 14 games and came at the right time for United who were then able to concentrate on stifling Arsenal's efforts.
The home side never quite got their game flowing. The stop start fragmented play owed much to the harrying and closing down by Alex Ferguson's hard working side.
Wenger then brought on van Persie on 65 minutes to mount a three pronged attack and the move paid dividends. Suddenly United looked stretched and on 83 minutes the Dutch striker was on hand to level the scores.
The move became dangerous when Tomas Rosicky found space on the right and got past Evra to deliver a ball into the area. Henry connected with a light back heel that allowed van Persie to slide in on the far post ahead of Neville to fire the ball high into the United net.
The Gunners then smelt blood and seemed to grow in confidence and attacking ambition and added to their forward line by replacing Mathieu Flamini with Julio Baptista.
United on the other hand looked more keen to preserve a share of the points, which was evidenced by the substitution of Cristiano Ronaldo by defender Gabriel Heinze.
The Gunners got their reward for their endeavour in the dying minutes when Eboue exchanged passes with Rosicky before delivering a peach of a cross that Henry headed home powerfully.
The Celebrations in north London were loud, but they must have been matched by the relief felt in the south of the capital.