Lallana, who has been with Saints since he was 12 and witnessed at first-hand their slide from the Premier League, via administration, to the foot of the third tier, struck with a superb curler to leave the Premier League visitors sweating.
But two goals in three minutes from Bowyer, 32, and 35-year-old Carsley - Blues' first goals from open play this season - saw Alex McLeish's side safely through.
McLeish made seven changes to the side which drew with Stoke on Saturday, but injuries throughout the squad meant this was no weakened line-up and also meant he could only name five substitutes.
Hong Kong billionaire Carson Yeung is apparently close to completing his takeover of the club, and his promise of £5million to spend before next week's transfer deadline could come in very handy on this showing.
Few eyebrows were raised when Southampton won this fixture 2-0 at the same stage of last season's competition, when both teams were in the Championship.
But the clubs have moved in opposite directions since, with City enjoying a solid start to life in the Premier League and Saints floundering on minus eight points at the foot of League One - some 60 places below.
Yet it was Southampton who made the livelier start, with youngster Lloyd James hooking a shot over the crossbar and recalled City keeper Maik Taylor foiling Marek Saganowski as the Polish striker raced through.
Chelsea loanee Jacob Mellis fired wide from the angle and £1million frontman Rickie Lambert missed his kick when well placed with the hosts making all the early running.
They also had a decent penalty shout waved away when Mellis appeared to be fouled by Franck Queudrue.
But Christian Benitez, the Blues' £7million record signing, exploded into life in the 28th minute of his full debut with a rasping 20-yard drive which beat home keeper Kelvin Davis, but not his right-hand post.
The ball pinged straight back out to Gary McSheffrey, who could not control his effort and volleyed over.
At the other end Lambert shot straight at Taylor, but the visitors were by now looking more menacing and Chris Perry did well to block Bowyer's low cross with McSheffrey lurking.
Sebastian Larsson thought he had given City the lead with a curling free-kick but Davis flung himself across goal to make a fingertip save.
Davis also kept out a low shot from the Swede after he was teed up by Stephen Carr as the interval approached.
But it was Saints who took a shock lead in the 52nd minute through Lallana.
The young midfielder is a product of the academy which brought us Theo Walcott, Kenwyne Jones and Gareth Bale and is apparently also on the radar of a number Premier League clubs.
He showed why when he collected a loose ball 18 yards out after Larsson had been dispossessed and dispatched a superb curler past Taylor's despairing dive and into the top corner.
Birmingham attempted to hit straight back and Davis made another fine stop to deny McSheffrey from the edge of the area.
Saints had to readjust when Graeme Murty was taken off on a stretcher with suspected knee ligament damage following an innocuous-looking challenge, while City threw on James McFadden and Garry O'Connor.
Mellis almost doubled Saints advantage when he wriggled free down the right but Taylor kept out his angled shot with his legs.
And moments later, in the 77th minute, Birmingham hauled themselves level when Benitez played in Bowyer to clip the ball past the helpless Davis and into the net.
Davis saved another fierce shot from Benitez, but he could do nothing when Stuart Parnaby's low cross was sidefooted into the net by Carsley in the 80th minute.
Brum had to survive seven minutes of stoppage time, courtesy of Murty's injury, but the weary Saints by then had little left to offer.