Striker Phillips had only been on the pitch for less than a minute against his former club when he pounced to smash the ball home from close range.
Phillips scored the winning goal in last Saturday's 1-0 win over Sheffield United and repeated the trick for the second week running.
Former Birmingham striker Stern John had the game's first opportunity in the seventh minute.
Midfielder Simon Gillett crossed from the left and John flicked the ball goalwards only to see it go just wide of the right-hand post.
Garry O'Connor had Birmingham's first chance in the 24th minute but made a complete hash of his opportunity.
Striker O'Connor was left with an empty goal four yards out but mis-hit his shot and Southampton's left-back Andrew Surman was able to clear the danger.
Southampton took the lead in the 43rd minute with Chris Perry's first goal for the club since his move from Luton Town last season.
Lee Holmes put over an inviting corner and Perry ghosted in at the far post to head the ball home from two yards.
The lead did not last long and Birmingham soon equalised four minutes into the second half.
Defenders Perry and Michael Svensson made a complete hash of clearing the ball and it fell to O'Connor, who raced through the defence before beating Kelvin Davies with a low shot that went into the bottom left-hand corner.
Substitutes Cameron Jerome and Marcus Bent were causing the Southampton defence all sorts of problems and it was no surprise when fellow sub Phillips grabbed the all important winning goal.
Bent headed the ball goalwards and Davies made the save, but Phillips was on hand to smash home the winning goal in the 77th minute.
The diminutive striker rammed the Southampton fans' boos down their throats as he celebrated with the Birmingham supporters behind the goal.