The reaction from Town wasn't long in coming howeverm and within a few minutes of the restart, Irish midfielder Cathal Lordan launched a shot from around 30 yards out into the back of the net to bring the scores level.
It was Lordan again who was to score to put Town ahead just before the hour mark with a low shot past the Southampton keeper after good work by Darryl Knights who made his first team debut as a substitute earlier in the season for the blues.
However the Saints hit back through Leon Best shortly after Town took the lead when Town's Irish keeper Shane Supple was unable to hold on to a Walcott attempt on goal, of which the rebound was struck home by Best after Synnott failed to fully clear.
Town go into Friday's second leg at Portman Road as slight favourites, having no disadvantage to overturn in the home leg, with a strong home crowd expected to behind them, Town look to be in with a good chance of lifting their third FA Youth Cup in their history.
Youth Side: Supple, Moore, Synnott (Haynes 61), Krause, Casement, Collins, Lordan, Trotter (Sheringham 90), Knights (Hammond 86), Craig.
Click here for Match Photos from the game.