Eniola Aluko scored twice as Charlton broke their Arsenal hoodoo to lift the Nationwide Women's Premier League Cup.
Aluko struck twice in the first half
The Addicks had lost to the Gunners in cup finals twice in the last two years.
Aluko put Charlton ahead, lobbing Emma Byrne, before Addicks keeper Pauline Cope made good saves to thwart Julie Fleeting and Lianne Sanderson.
England striker Aluko struck again after a mistake by Alex Scott before Fleeting pulled a goal back after a flick from Anita Asante.
In successive seasons the Addicks lost to Arsenal in the FA Cup final then in last season's League Cup final.
But the first-half brace from 19 year-old Aluko, who hit Charlton's match-winner in last season's FA Cup final against Everton, made it third time lucky for the Addicks.
Charlton captain Casey Stoney said: "Work rate and team spirit got us through but if we've got Eni in our team we can win any trophy because she tears defences apart."
Arsenal controlled the majority of the game but Fleeting's goal 14 minutes from time proved no more than a consolation.
The Gunners might have had a penalty in stoppage time, when Fleeting went down in the area, and manager Vic Akers was not impressed with the referee's decision.
"It was a nailed-on penalty," insisted Akers.
"The referee had a poor game but we were disappointing at both ends of the pitch.
"We had 80% of the play but you cannot defend the way we did in the first half and come out unscathed."
Arsenal had the better of the early exchanges and both midfielder Jayne Ludlow and left winger Rachel Yankey went close to scoring.
But the Gunners then went behind to a finely executed 28th-minute goal, which was set up by right-back Stoney.
The skipper hoisted the ball forward for Aluko to outpace her England colleague Mary Phillip before lobbing Byrne.
After Aluko's second in first-half stoppage time, striker Amanda Barr almost netted a third goal for the Addicks four minutes after the break, her 12-yard volley flashing wide of the far post.
Arsenal quickly regained territorial advantage, however, and Cope had to make goal-line stops from Kelly Smith and Fleeting.
Cope was finally beaten in the 76th minute, Fleeting scoring from 12 yards following a Ludlow pass.
But despite late pressure and their stoppage-time penalty claims, the Gunners rarely looked like forcing the game into extra time.
Charlton manager Keith Boanas said: "We had to shuffle our pack because of injuries but our gameplan went as I wanted in the circumstances.
"Arsenal will be out for revenge big time when we play them in the FA Cup semi-final in a fortnight but I had a gut feeling we would beat them today and hopefully we can do it again."
Arsenal: Byrne; Tracy, White, Phillip, Scott; Asante, Ludlow; Smith; Sanderson, Fleeting, Yankey (McArthur 77).
Substitutes not used: Pealling, Champ, Grant, Larkin.
Charlton Athletic: Cope; Stoney, Bertelli, Hills, Hickmott; Barr, Chapman, Pond, Potter; Snare, Aluko (Hincks 83).
Substitutes not used: Sinclair-Chambers, Cabey-Gooden, Adams, Cardin.
Referee: Mr P. Forrester (Bedfordshire).