The striker, who retained his place despite Kevin Phillips returning to the squad, struck four minutes from time to deny Charlton a famous come back.
The home side dominated early proceedings and were rewarded after only five minutes when Jason Dodd's corner was only half cleared to David Prutton and his shot was turned in by defender Michael Svensson as striker Jason Euell tried in vain to clear off the line.
Southampton had chances to double their lead, but found keeper Dean Kiely in good form as he denied both Rory Delap and Prutton.
Charlton posed little in the first period but keeper Antti Niemi had to be on his toes in the 23rd minute when he clawed away Paolo Di Canio's half-volley from a Euell knock down.
But the home side deservedly doubled their lead on the stroke of half time when Prutton fed James Beattie down the right and his cross was turned in by the impressive Ormerod at the near post.
The second half mirrored the first period although it was Charlton's turn to pose more attacking threat.
Only 30 seconds into the half, Charlton were back in the game when midfielder Scott Parker thundered a 20-yard shot into the top right-hand corner.
Midfielder Graham Stuart saw his shot hit the bar and the forced Niemi into a good save as the visitors searched for an equaliser.
The leveller finally came on 65 minutes when England hopeful Parker scored his second with a curling 25-yard effort into the same top right-hand corner.
The visitors nearly completed a dramatic comeback with a winner on 73 minutes, but Di Canio saw his stinging shot turned around the post by Niemi.
And it was rough justice on the visitors who deserved a point as Southampton stole the win four minutes from time.
Ormerod scored his second goal of the season from two yards out after defender Svensson had flicked a header goalwards.