It was a game where the scoreline didn't reflect the performance as the young Rovers pressed the home side all the way but for once their finishing let them down.
The Under-18s had netted 17 times in their six previous outings but they drew a blank against the Saints despite creating a host of chances.
David Lowe's side started promisingly on the south coast, Dean Rittenberg's free header well saved from just six yards out.
But despite that early pressure it was the Saints who opened the scoring on the quarter hour to leave Rovers chasing the game.
As they looked for a leveller Rittenberg was twice denied, whilst strike partner Jordan Preston also saw a goalbound effort well saved.
The second half continued in the same vein, substitute Sam Joel also going close to grabbing an equaliser.
However with Rovers pressing for a way back into the game, they were caught on two occasions late on with Southampton grabbing further goals to claim the win.
"We played very well for an hour without scoring from our numerous chances," said David Lowe.
"We had at least three or four clear cut chances but then we were caught with the sucker punch by conceding two late goals that didn't give a fair reflection of the game.
"It was very disappointing for the boys, we had a good go but unfortunately we couldn't score and paid the price at the back end of the game."
ROVERS: Raya, Anderson (sub Joel 65 mins), Langford, Butterwick (sub Tanner 70 mins), Lavelle, Wassi, Harris (sub Doyle 85 mins), Vicars (c), Rittenberg, Preston, Torres.
Subs not used: Scott, Pierce.