Rickie Lambert, Jay Rodriguez and an own goal by Andy Wilkinson had given Saints a 3-1 lead but 10-man Stoke hit back through Matthew Upson before Cameron Jerome's stunning 90th-minute equaliser.
The result dropped Southampton back into the bottom three but Schneiderlin said: "It was a crazy game. I think we are all a bit disappointed.
"When you look at the game we were 3-1 up, we could have scored the fourth one and we could have killed the game off.
"But I think before the game everyone would have been happy with one point and we need to take the good things. You don't have a tougher place to go in the league than Stoke City and it's a good point."
Schneiderlin also admitted Saints were lucky to get away with what should have been a penalty after Jose Fonte handled the ball in a challenge with Kenwyne Jones.
"I'm going to be honest and I'm going to tell you it was a handball," said the Frenchman. "But for the (third) Stoke City goal it was a handball as well, Peter Crouch controlled the ball with his hand, so it's 50-50."