
Chasetown led at half time when Jack Langston's free kick sailed beyond the head of goalkeeper Tommy Jackson.
Dan Beddows with a second half header could have put Chasetown two goals to the good but the Scholars were unable to add to their earlier lead.
Walsall came back strongly in the final quarter of the game and levelled with three minutes remaining when Danny Coogan's effort flew beyond Curtis Pond.
Pond saved the first two Walsall penalties, with Chasetown leading 1-0 from the spot through Levi Reid. Langston had the second Chasetown penalty saved before Walsall scored their third and Pond scored to give Chasetown a 2-1 lead.
Walsall's next two were netted but both Kieran Brown and Joe Brown were off target as Walsall won 3-2 from the spot.