Antony Kay drove home his sixth goal of the season in injury time from an Ian Moore pass to secure a dramatic win for Tranmere at Prenton Park.
Ian Goodison had put the hosts in front three minutes before the break from a mishit shot by Chris Shuker.
But Goodison tripped Jabo Ibehre in the box after the interval and Marco Reich equalised from the spot.
Kay had missed two good chances, one just before the end of normal time, before hitting the winner.
Tranmere: Coyne, Edds, Chorley, Goodison, Taylor, Shuker, Jennings, Kay, Sonko (Cresswell 65), Moore, Savage.Subs Not Used: Achterberg, Antwi, Barnett, Henry.
Goals: Goodison 42, Kay 90.
Walsall: Ince, Palmer, Weston, Gerrard, Sansara, Reich, Mattis, Taundry, Nicholls, Ibehre, Deeney.Subs Not Used: Gilmartin, Smith, Davies, Grigg, Adkins.
Booked: Sansara.
Goals: Reich 54 pen.
Att: 5,913
Ref: Lee Probert (Wiltshire).
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