Despite a magnificent performance from Scott Parker, who scored twice and cleared off his own line, it was settled five minutes from time by Brett Ormerod's second goal of the game for Southampton.
Charlton's fighting qualities and Parker's superb shooting were very much in evidence as they fought back from a two-goal first-half deficit only for Ormerod to crush their comeback with the winner.
The former Blackpool striker was among 10 Saints in the starting line-up without a Premiership goal to his name, but the previously goal-shy Saints scored three while their usually parsimonious defence, through no fault of their own, let in two in a Super Sunday classic as enjoyable as it was unexpected.
Five Premiership games without a goal, Southampton were celebrating within five minutes. With Charlton unnerved by their hosts' aerial ability at set pieces, Rory Delap had room to shoot and Michael Svensson touched it over the line.
And it was a very different Southampton side from the sterile outfit of the past two months, helped by Gordon Strachan's team selection. Out with the apathetic Anders Svensson and Neil McCann; Ormerod was partly responsible for the high tempo and excitement.
David Prutton joined Southampton in January, but this was just his third start of the season. The England Under-21 international midfielder provided an injection of energy into the Southampton midfield, proving his point to Strachan with fierce tackling.
Both Prutton and his centre midfield partner Rory Delap got forward to draw superb saves from Dean Kiely with long-range efforts. As importantly, their industry allowed Marian Pahars greater freedom on the left flank in his first start for 13 months.
And Prutton was involved in Saints' second. He played the pass behind left back Hermann Hreidarsson. Beattie, bursting with determination, supplied the cross from the byline and the ever enthusiastic Ormerod sidefooted in his first of the season.
Paolo di Canio - overshadowed for once - and Hreidarsson missed the target for Charlton, but their finishing was altogether better in an end-to-end second half. On the day of the FA Cup draw, this was more reminiscent of a classic cup tie.
Parker scored a wonder goal when these two teams last met. He added two more at St Mary's; though he has been criticised for a lack of goals, there is no shortage against Southampton.
His first, a minute after half time, was unstoppaable and vindicated Alan Curbishley's decision to send his side out early after the interval. The second, a curler, left Antti Niemi motionless and Sven Goran Eriksson smiling.
Parker's long-range shooting inspired his team-mates. Graham Stuart hit the bar, Radostin Kishishev volleyed just over and the flying Niemi kept out both Stuart and di Canio.
The ubiquitous Parker then found time to clear off his own line and deny Claus Lundekvam a first goal in a Southampton career, spanning 285 games and seven years.
Then Stuart, on sentry duty on his post, saved Charlton from a Svensson header, but when Ormerod latched on to a Beattie header, neither he nor Parker could save Charlton.
