Young midfielder Richie Ryan was shown a straight red card for a challenge on Simon Osborn and that left the home side facing an uphill battle against the lively Saddlers.
Scunthorpe had already fallen behind but they looked very much off the pace for long spells with only Nathan Stanton and Matthew Sparrow looking anything like on form.
Walsall boss Paul Merson may have lost some of his pace but his skills were often demonstrated and his passing stretched the home defence, while Chris Westwood was a strong figure at the back.
Walsall dominated the opening stages and on one occasion needed the resources of skipper Andy Crosby and Stanton to halt a threatening move from Matt Fryatt.
Jorge Leitao then found himself forcing his way through the middle and Paul Musselwhite had to go full length to save.
Walsall's pressure brought them the opening goal from the penalty spot after 15 minutes.
Richard Hinds' challenge on Leitao was judged to be unfair and Fryatt scored to Musselwhite's left-hand side.
Scunthorpe responded with Ian Baraclough's free-kick being touched on to a post and out of play by John Ruddy - on-loan at the Saddlers from Premiership side Everton.
The game was held up for a couple of minutes when referee Russell Booth showed Ryan a straight red card in the 20th minute for an alleged elbow on Osborn who also received a yellow card - and Crosby received a similar colour for his protests.
Matthew Williams tried his luck from a central position, hitting a long-range screamer from 35 yards just over the top.
Billy Sharp then forced his way into the box and his shot was blocked.
The Saddlers almost grabbed a second goal in the 52nd minute when Paul Smith's cross reached Fryatt and he lifted the ball over from close range.
That miss looked costly when Scunthope grabbed an equaliser three minutes later.
Baraclough forced the ball through the right channel for Andy Keogh to clip it into the six-yard area and Sharp headed home from close range.
But that failed to last long as Walsall stretched the home defence twice inside nine minutes.
Osborn scored with a sharp chip shot over Musselwhite and he grabbed his side's third in the 75th minute scoring at ease with a right-foot shot to give the keeper no chance.