The Saddlers conceded inside the first 30 seconds after Rollin Menayese put through his own net, his first appearance since signing permanently from Mansfield Town.
Boro winger Chris Lines then found himself free at the back post to head home, with ‘keeper Carl Rushworth unable to palm away the effort.
Brendan Kiernan grabbed Walsall's only goal of the afternoon before Jake Taylor picked up a third for the visitors in added time.
Dismal defending from the Saddlers
Matthew Taylor's side conceded their sixth goal in two games after another messy defensive performance.
Following the entertaining 3-3 score draw against Newport County, Saddlers fans were hoping that there would be a more cohesive display from the back line.
This wasn't to be as full-backs Stephen Ward and Zak Mills found themselves beaten all ends up by the Boro wingers throughout the first half.
The former, despite his experience, found himself wandering for Stevenage's second, whilst the latter was out-jumped to allow Lines to head home.
At centre-back, Menayese didn't have the best start to his permanent Saddlers career, deflecting Luke O'Neill's cross past Rushworth to open the scoring.
The Welshman could've made amends for his error at the other end but headed agonisingly wide from a set-piece before the game's end.
Hayden White found himself in the middle of the back-line, away from his natural right-back position, but did look more positionally sure during the second half after a shaky first.
Young shot-stopper Rushworth will have also felt he could've done more about Boro's second, as he got considerable contact on the ball, but pushed the header straight into the net.
Strugglers Stevenage have found themselves with little to cheer about so far this campaign.
However, with thanks to the Saddlers’ defensive gifts, Boro scored three in the league for the first time this season.
Ending a run of seven without a win, Paul Tisdale's men looked incisive and sharp on the counter, with plenty of wit and guile to create opportunities in forward areas.
It's easy to say that if they continue this type of form, they'll have no issues surviving after pushing themselves up to 21st in League Two.
Groundhog day for Walsall
This loss has all the hallmarks of previous defeats for Taylor's men.
And with those two outfits and Stevenage both below them in the league table, it's imperative Walsall cut out these league defeats in order to string together some momentum.
The Saddlers are more than capable of keeping the ball but found themselves unable to do the simple things right in this one.