Former England Under-21 captain Prutton had long been linked with a move a way from St Mary's after a 2006 blighted by a succession of injuries.
Prutton was on the verge of joining Leeds United in the summer only for the midfielder to fail a medical and his Saints contract expires in June next year.
The midfielder did his best to convince Burley he is worth hanging on to by netting his first league goal since January 2005, on 53 minutes to add to Pele's early opener.
The game was forced to be delayed by 45 minutes after a torrential downpour enveloped the city an hour before kick-off.
Predictably the first half was an equally grey and damp display by both teams, livened up only by Pele's header on nine minutes.
Nathan Dyer evaded Nils-Eric Johansson and pulled the ball back for Alexander Ostlund to cross on to the Portuguese midfielder's head.
Pele was forced to move away from goal to redirect Ostlund's powerful centre into the top corner for his first ever goal for Southampton.
On 36 minutes the lively Dyer was taken off with a suspected broken ankle after being clattered by Danny Tiatto.
The burly Australian escaped punishment and then five minutes later was lucky to stay on the pitch when he reacted to substitute Prutton's over-exuberant challenge with a sneaky headbutt away from the referee's gaze.
It proved irrelevant though as Southampton increased their lead eight minutes after the break when the impressive Bradley Wright-Phillips found Prutton at the far post.
Initially the midfielder's header was saved by Paul Henderson, but the ball ricocheted back on to his thigh and past the unlucky Foxes goalkeeper.
Southampton then stepped up into fifth gear and went close through Wright-Phillips, Rudi Skacel and then substitute David McGoldrick, but each time Henderson saved the Foxes.
Leicester, by manager Rob Kelly's own admission, were poor and failed to muster a shot on target all game.
Their only real opportunity fell to replacement Matty Fryatt four minutes from time, he hooked his close-range effort wide from a tight angle and by that time the game was already lost.