The goal was made by a fine run from Kris Taylor whose pass found Chris Westwood.
The full-back in turn fed Mark Wright, whose intended left-footed cross bypassed everyone, and went in off the far post.
Walsall were reduced to ten men in the 29th minute when on-loan striker Tommy Wright received a straight red card from referee Andy D'Urso for a two-footed tackle on Stuart Drummond. In the commotion that followed, Walsall's physiotherapist Jon Whitney was lectured by the referee.
It was a result that the League Two leaders could hardly have dreamt about during the first half in which Shrewsbury, spurred on by former Walsall youth midfielder Ben Davies, and looked the better side for long periods.
Ironically, it was Tommy Wright who seemed the most likely to score for the Saddlers, having a fourth minute header go over from Taylor's cross and another go wide in the 24th minute, also from Taylor's cross.
At the other end, Shrewsbury striker Andy Cooke saw a 39th minute header go off target and a shot by Davies four minutes before the interval was deflected for a corner from which defender Sagi Burton had a header go wide.
It was a disappointing first period, but when Craig Pead came on for Tony Bedeau straight after half-time, Walsall sparked into action, took on the offensive and eventually deserved the victory.
Daniel Fox had a 55th minute free-kick sail narrowly wide and Martin Butler's diving header failed to trouble keeper Scott Shearer from a good cross by Mark Wright.
Shrewsbury made a double substitution in the 74th minute. On came big striker Leo Fortune-West for Cooke and Danny Thomas replaced midfielder Ben Herd.
But with keeper Clayton Ince handling superbly and Scott Dann starring in the middle of the defence, Walsall were sad and troubled although Dann headed against his own bar in the 89th minute.
Prior to that, however, Mark Wright, Westwood and Dann all had shots blocked in quick succession as Walsall finished the match the better side.