Boro came back from a goal down to go in all square at half-time, thanks to Anthony Peacock. David Wheater grabbed the winner early in the second half.
The victory last night means the Youth side will be at home to Newcastle United in the next round.
Boro Team v Walsall
Knight, McMahon, Masters (Cattermole), Bates, Liddle, Wheater, Taylor, Kennedy, Peacock, Craddock, Morrison
Subs not used: Roberts (g), Johnson, Hines and Clough