The Saddlers, following the sacking earlier in the week of manager Paul Merson, twice found themselves behind and adding to their worries was a 69th minute red card for experienced winger Paul Devlin for using an elbow on Steve Foster.
Devlin will now miss three matches as Walsall shape up for a very difficult run in towards the end of the season.
Andrew Barrowman, who notched Walsall's late equaliser, was the only man to really trouble visiting keeper Tom Evans.
In the 14th minute the young on loan striker saw a shot tipped over the bar by Evans following a pass by Mads Timm.
Scunthorpe took the lead in rocky fashion in the 19th minute. Timm appeared to be comfortably controlling the ball in midfield when he collapsed in agony with a back injury and Andy Keogh was quick to seize possession, beating keeper Andy Oakes with a great 25-yard shot.
Scunthorpe looked to be taking control but Dean Keates, who has resumed his career with Walsall after four years elsewhere, made an impact in the 30th minute.
Scunthorpe failed to deal with a high ball and Keates took possession before firing a great shot over the helpless Evans.
The little midfield dynamo was only just wide with a free-kick two minutes before the interval but Scunthorpe restored the lead in the 45th minute.
The goal came as a result of a well rehearsed free-kick with Michael Rose shaping up to take it, pulling out at the last second and leaving Jim Goodwin to push the ball short for Neil MacKenzie to score with a shot from just outside the box.
Scunthorpe were generally the better side in the second half, although Barrowman had a shot saved by the alert Evans.
Oakes somehow kept out a fierce cross-shot from Cleveland Taylor to keep Walsall in the game after 74 minutes and three minutes later the Saddlers snatched an equaliser.
It was another high ball which Scunthorpe were unable to clear, Pablo Mills pumping a long pass up for Barrowman to send a 15-yard shot sweetly over Evans.
In the 83rd minute Oakes made an unbelievable double save, firstly from MacKenzie's shot and then from a follow up header by Matt Sparrow which looked certain to go in.
At the other end Keates almost crowned a tremendous home debut on his return with a shot that hit the Scunthorpe bar and bounced to safety.