The win came despite playing the second-half with 10 men, after David Prutton was sent off for the second time during his loan at the club, and ended an eight-game winless run.
The Iron were already leading by two goals and even with 10 men added two more in the second half against a young and injury-hit Walsall side, now without victory in nine games.
Scunthorpe took control from the start and went ahead after 13 minutes when a Mark Duffy corner was headed in at the far post by central defender Niall Canavan, who was only in the side due to an injury to David Mirfin.
The visitors added a second after 30 minutes when Mark Duffy tapped in after Karl Hawley's shot had been blocked, and a minute from half time Scunthorpe midfielder Prutton was red carded for a crunching tackle on Adam Chambers.
Despite the Saddlers holding a numerical advantage, the visitors added two more in the second half.
The first was another Canavan header from a Duffy corner, after 50 minutes, before Leon Clarke added his eighth of the season with a chipped effort over keeper David Grof with 15 minutes to go.