Henry, who had missed the last eight games with a mystery sciatica problem and fatigue, coolly converted a 30th minute penalty to set Arsenal on their way to an easy victory that puts them back into a Champions League positions.
A deflected shot from Cesc Fabregas was tipped on to the underside of the crossbar by Charlton goalkeeper Scott Carson and in the chase for the rebound Osei Sankofa tugged the shirt of Robin van Persie right under the nose of referee Mike Riley.
As Sankofa departed with a red card, Henry rolled his penalty to Carson's left to score his eighth goal of the season and took him to 198 Premiership goals in his glittering Gunners career.
His celebrations were also significant. The Frenchman ran straight over to Wenger to prove their relationship is still strong.
The pair had a row when Wenger decided Henry needed to rest and couldn't play in the north London derby against Spurs on December 2.
Arsenal couldn't have wished for better opposition after their defeat at Sheffield United on Saturday. Charlton are firmly rooted in the relegation zone and were forced to play without top-scorer Darren Bent, who could miss four weeks with a knee injury.
Predictably it was one-way traffic and the only surprise was that it took Arsenal so long to break the deadlock.
Philippe Senderos went close with a header, Fabregas had an effort tipped over by Carson and then Henry hit the post with a header.
And once Arsenal went ahead it was a case of how many they would score.
Carson pulled off a brilliant save to deny Henry as his shot arrowed towards the top corner, but it was a less likely goal source that put Arsenal two ahead on the stroke of half-time.
Full-back Justin Hoyte, the only Englishman in the Arsenal side, made a surging forward run, played a one-two with Henry and beat Carson with a terrific shot from an acute angle. It was the 22-year-old's first goal for Arsenal and was marked with three joyous punches of the air and a little jig of delight.
The second half was all Arsenal as you would expect. Tomas Rosicky should have scored after a flowing move but hit the woodwork with his final shot.
Henry then put the ball in the net after a great move involving Aleksandr Hleb and Rosicky but was judged offside. The French striker was then denied by a goalline clearance from Talal El Karkouri.
Carson then saved brilliantly from Fabregas and Henry as Arsenal ran riot without getting their full reward in goals.
The inevitable third came after 76 minutes when van Persie released Henry and he was tripped by Souleymane Diawara. Van Persie asked his captain if he could take the penalty and after the request was granted, the Dutchman buried the penalty for his 11th goal of the season.
Number 12 then came right on full-time when he swept home a pass from substitute Matthieu Flamini from 12 yards.