Stevenage succumbed to a third successive defeat as Walsall winger Jamie Paterson struck a brilliant late winner at the Banks's Stadium.
The referee played advantage when Sam Mantom was fouled and Paterson found the top corner with his left foot.
Boro looked sharp prior to the break as Filipe Morais tested Karl Darlow before rattling the bar with a free-kick.
But Walsall raised their game after the interval, Will Grigg twice going close before Paterson fired the winner.
The downside for the Saddlers after their third win in four games was losing on-loan midfielder Florent Cuvelier with another hamstring injury.
VIEW FROM THE DRESSING ROOM
Walsall manager Dean Smith told BBC WM:
"It was hard going in the first half but I thought it was merited in the end against a Stevenage side who are well organised and tough to break down.
"And it took a special goal from Jamie Paterson to win it. He's in a rich vein in form and he knows where the back of the net is.
"We're in a good run of form and that should gee the lads up for the televised game against Portsmouth on Friday night."