Keith Bertschin's side also had to overcome playing with just ten men for 40 minutes of the second half after James Blake was sent off for two bookable offences.
The hosts took the lead just three minutes before the half time break through former Leeds United and Huddeersfield striker Clyde Wijnhard who is on trial with The Saddlers.
Blake received his marching orders five minutes into the second period but Blues equalised on 64 minutes through Peter Till.
Walsall Res 1 Blues Res 2
Blues took a 2-1 lead with just a minute to play through defender Krystian Pearce and they managed to hold on for their first win of the season despite conceding a stoppage time penalty which Saddlers striker James Constable put wide of the post.
Blues: Meredith, Howell, Blake, Oji, Pearce, Asa Hall, Till, Kilkenny,Aluko, Allen, Birley. Subs: Hinks, Mark Hall, Skeldon, Price, Wright.
Blues: Meredith, Howell, Blake, Oji, Pearce, Asa Hall, Till, Kilkenny,Aluko, Allen, Birley. Subs: Hinks, Mark Hall, Skeldon, Price, Wright.