The Saddlers claimed only their second away win of the season.
Belgian teenager Florent Cuvelier, on loan from Stoke, bagged the only goal of the game to dump the Iron back into the bottom four with only their second defeat in eight games.
A poor first half did not come to life until the half-hour mark when Cuvelier pounced on an error from centre-back Paul Reid but lashed his shot well wide of target.
But he made no mistake four minutes later as he broke the deadlock with his second goal in three starts, pouncing as two Scunthorpe defenders dithered on the edge of their own box before drilling an excellent shot low into the far bottom corner.
The home side pressed strongly to try and get back on level terms by half-time, with striker Jon Parkin twice going close and fellow frontman Garry Thompson missing a good chance. Parkin then fluffed a great opportunity early in the second half when he scuffed his shot inside the six-yard box.
Walsall defended well in depth to deny the home side who could not find their finishing touch in front of goal. But the visitors did need one excellent save in the closing stages from goalkeeper David Grof to keep out a stinging shot from midfielder Josh Walker, while at the other end Cuvelier almost snatched a second for Walsall.
