The teams fought out a goalless draw in difficult conditions at St Mary's, although things could have been much different had the French midfielder been sent off.
Allardyce felt Schneiderlin should have been dismissed for a poor first-half tackle on Mohamed Diame, for which Marriner did not even award a free-kick.
West Ham themselves were fortunate not to be reduced to 10 men after a Joey O'Brien lunge on Adam Lallana with 20 minutes remaining, but Allardyce feels Schneiderlin's tackle would have been the difference.
"We feel a bit disappointed that Schneiderlin is still on the pitch - we didn't even get a free kick - because it's a two-footed challenge," the Hammers boss told Sky Sports 1.
"(With) two-footed challenges, we have been told by everyone in the referees' department from Mike Riley down, there is no other choice but a straight red - this one we didn't even get a free kick.
"I can't for the life of me [understand] - Andre (Marriner) is such an experienced referee now, how he didn't see that.
"For me that was a disappointment. It's in the end kept them with 11 men on the field when the law was supposed to be they should only have had 10 men which would have given us a better chance of winning.
"But I'm happy with a point. I can't affect what the referees do, it's not my job."
In the end, Allardyce had goalkeeper Jussi Jaaskelainen to thank for keeping the Saints at bay.
The oldest man on the pitch produced fine saves to deny Dani Osvaldo, Schneiderlin and Rickie Lambert, who also hit the post minutes into the second half.
Those missed chances almost allowed West Ham to snatch a late winner, only for the otherwise impressive James Collins to blaze over.
"We could have won it at the end when the chance he had was probably our best chance of the game, unfortunately for him it's fell to the centre half," Allardyce said.
"At the end of the day that far out he should at least hit the target but overall (it was) a decent performance.
"Defensively we showed how good we are, I think we have only conceded one goal in four games, but we just can't find the back of the net.
"Three games without a goal is my concern - it's not as if we haven't created any chances or good opportunities in and around the final third today to try and score but it's just eluding us at the moment.
"When a golden chance falls that late in the game you want to put it in and walk away with all three points."