In a tense and largely mediocre meeting between the two sides starting the day in the bottom two places in the table, Aguerd's first-half header settled a contest devoid of attacking quality throughout, allowing David Moyes's side to jump up five places to 14th while the Saints remain rooted to the bottom of the rankings.
While there were some fleeting glimpses of West Ham threat early doors, the opening 10 minutes were nothing to write home about - arguably to be expected between two sides fighting for their lives at the foot of the table.
Ruben Selles's side had started to enjoy a steady period of possession as the first half progressed, but a disastrous attempt at defending an outswinging Thilo Kehrer free kick saw the visitors concede first on the 25-minute mark.
Kehrer's set piece found fellow defender Aguerd, who rose head and shoulders above those in white to direct a header into the bottom corner, although the flag initially went up for offside.
However, following a VAR check lasting a good few minutes - to the ever-growing frustration of both sets of supporters - the goal was given, and Aguerd wheeled away in celebration for the second time.
Southampton responded well to going behind, and left-back Romain Perraud stung the palms of Lukasz Fabianski in the 32nd minute, with the recalled West Ham number one equal to his low attempt from just inside the box.
Perraud would nearly be left to rue that squandered chance, as Jarrod Bowen cut inside from the left and tried to pick out the top corner in added time, but the attacker's curling effort struck the crossbar and sailed behind.
Selles held off on making any half-time changes, but the Saints boss soon relented and called upon Carlos Alcaraz and Kamaldeen Sulemena - the latter of whom brought a new dimension to the attack straight away with his driving runs at the West Ham backline
Sulemana fired wide in the 57th minute as Southampton tried to force the issue, while Romeo Lavia and Alcaraz were both denied by Fabianski in a two-minute spell during the best period of the game for the visitors.
Having come through that brief period under the cosh unscathed, West Ham looked the more likely to net the game's second goal during the next 15 minutes, and Gavin Bazunu was called upon to beat away Said Benrahma's top corner-bound free kick in the 75th minute.
Lucas Paqueta was presented with a gilt-edged chance to wrap the game up in the 82nd minute, with the ball falling to the Brazilian at the back post from a corner, but he could not keep his effort down and fired over from couple of yards out.
Despite showcasing a distinct lack of ruthlessness all afternoon, Southampton came agonisingly close to drawing level through Paul Onuachu in the 86th minute, but the towering marksman rattled the bar with a header from James Ward-Prowse's delivery before Kyle Walker-Peters curled over on the rebound.
More to follow.