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.