Lee Bradbury duly converted the spot kick and Walsall headed back to the Midlands with all three points.
"You hope to get that little bit of luck and we got it today," Lee said after the game.
"The decision was controversial because the linesman, I believe, saw it differently to the referee. I would be disappointed if I was in their camp.
"The linesman put his flag up and I must admit that is hard to swallow when you are down at the bottom, but we have had many decisions go against us over the season."