Kris Commons headed the Parkhead side into the lead in the sixth minute before he was carried off on a stretcher just before the break with an ankle injury after clashing with team mate Beram Kayal.
The home side had the ball in the net in the first half from a Gary Teale cross only to have it ruled out for Paul Dummett's challenge on Hoops keeper Fraser Forster.
They then had a good penalty appeal turned down moments from the interval when the ball appeared to hit the arm of Celtic's stand-in skipper Georgios Samaras.
Wanyama, back from suspension, was shown a straight red card 10 minutes into the second-half for a challenge on Paul McGowan, who levelled from the spot with 10 minutes remaining after Emilio Izaguirre was adjudged to have fouled Esmael Goncalves in the box, when it looked like there was little or no contact.
The Hoops boss admitted his concern for the "standard of refereeing" in general but first turned his ire on Madden.
"That was the most appalling refereeing performance I have seen for a long, long time," he said. "I mean, you can't get so many big decisions so wrong, it is incredible.
"For me St Mirren should have had a penalty, it is a clear handball.
"You don't get many more as clean-cut as that so we dodged a bullet there.
"Then I see Kayal getting wrestled into the advertising hoardings right in front of the linesman and he doesn't give a free-kick and two seconds later, I've got a man sent-off for nothing and the penalty that St Mirren did get was outside the box and there is no contact."