Tony Watt scored a quickfire second-half brace to seemingly put Motherwell in control but Eamon Brophy scored two goals of his own to earn his side a share of the spoils in a 2-2 draw.
Brophy pulled a goal back in the 74th minute before he won and then scored a spot-kick at the second attempt following a retake.
But Alexander was furious with the decision to award a penalty following a challenge from Sondre Solholm Johansen.
Alexander said: "I genuinely don't know what to say about the penalty decision because I want to do my job and I want to be honest, but I also want to work next week with my team so I can't say exactly how I feel as we are powerless. I think it was blatant for everyone to see and we've been punished tonight.
"Penalty decisions like that don't even come around every year never mind every week and I can't explain these decisions. Unfortunately, we can't control these decisions, so we will focus on our efforts and what we can do better."
Alexander did admit his side had been fortunate to find themselves 2-0 up early in the second half.
He added: "We had a 2-0 lead in a game that we weren't in control of as I thought St Mirren were the better team in the first-half.”
St Mirren boss Jim Goodwin praised his side's character and believes lesser teams would have left a game like that with nothing.
He said: "I felt as if it was a one-sided 45 minutes and we were in complete control. Unfortunately, we lost two goals in a five-minute spell.
"It's the reaction of the players I am satisfied with, as you can begin to think that it's not going to be your night, but huge credit to the boys who kept passing and probing and the opportunities eventually came.
"I'm delighted for Eamonn Brophy. It was an incredible finish from such a tight angle for the first goal before showing a lot of bottle to take the second penalty and dispatch it in the way that he did.
"I should be happy with a point away from home against a team who're fighting for their lives but I can't believe that we have not won that game as we absolutely dominated it."