Ashley Fletcher put the Reds in front on 17 minutes, but Tom Bradshaw levelled 11 minutes later.
Five minutes after half-time. Barnsley were back in front via Josh Brownhill.
And on-loan winger Harry Chapman added a third Tykes goal on 56 minutes.
Victory puts Barnsley into sixth spot, after 11 wns in 13 games, three points ahead of Coventry City.
“It’s a great victory away from home at someone higher above us in the league,” said caretaker boss Paul Heckingbottom.
“The performance was a game of two halves. We were second best first half, but Fletch (Ashley Fletcher) scored a great goal in an area of the pitch we did say we would get some joy. Our analysts watched their games which is their job, and credit to them.
“They were fantastic goals and we know we have that quality in our team so it’s frustrating when we don’t show it. We know it’s difficult as the opposition set up to try and stop us now, teams are knowing our strengths and what we’re good at but I’m delighted for the lads.
“Fletch has done well since he has come back in the starting eleven, Browny (Josh Brownhill) did well all game and so did Harry Chapman. He was a threat on the counter attack, his understanding of the game was very good.
“He’s (Chapman) got a good head on young shoulders and the positions he took off the ball caused them problems. It was his anticipation and positioning that enabled him to counter and score a great goal.
“Walsall are a good team and they managed to get shots off on our goal which we thought we were a little bit loose at times and made it easy for them, but as a whole we were much better second half and deserved it.”
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