The Frenchman lunged into Mohamed Diame late in the first half of the Premier League stalemate at St Mary's Stadium, leaving the West Ham player in agony.
Schneiderlin was not even penalised for his tackle, which infuriated Allardyce, who saw his side withstand a barrage of Southampton attacks to claim a point.
And Allardyce, who was pleased with the result, could not hide his displeasure at Marriner's decision after the match.
He told Sky Sports: "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, which 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."
Allardyce is concerned about his side's lack of goals though, as he saw their scoreless run extend to three Premier League fixtures.
West Ham were slightly unfortunate that their best opportunity of the match fell to the feet of centre-half James Collins.
The Wales international smashed the ball over the bar in the latter stages and Allardyce felt he should have scored.
"We could have won it at the end when Ginge (James Collins) had his chance - that was the best chance of game," he told BBC Sport.
"It was a bit unlucky that it fell to our centre half, but from that far out he should hit the target.
"Overall, it was a decent performance. Defensively we showed how good we are but we can't hit the back of the net. That's my concern at the moment."
