Skipper Craig Pead was harshly red carded as Walsall slumped to a disappointing defeat despite an impressive late fight back.
Walsall, already hampered by a string of injuries, had skipper Pead sent off by referee Graham Salisbury for an innocuous incident.
Already trailing to a Paul Hayes' first-half strike, Walsall levelled before Barnsley restored their lead.
Despite the setback Paul Merson's men came close to grabbing a late equaliser.
But afterwards the Walsall boss blasted the referee for what he saw as a string of questionable decisions.
The home side were in front after 13 minutes when a Chris Shuker cross from the right was headed on by Marc Richards and Hayes beat Joe Murphy with an angled shot.
Murphy denied Barnsley a second with another impressive stop as Hayes shot on the turn.
Walsall failed to produce a first-half threat until the 44th minute when substitute Anthony Gerrard smashed a low shot from 25 yards but Nick Colgan saved well.
But referee Salisbury angered Walsall with his decision to red card Pead in the 56th minute.
Brian Howard went down under a challenge from Pead and as he was on the ground the Walsall man appeared to swing his foot but without making contact.
Matty Fyatt gave the visitors hope after 63 minutes when he found space to side foot a shot in.
The lead lasted just three minutes though before Howard shot from eight yards out after a Martin Devaney cross was deflected into his path.
In a final flurry Walsall rampaged forward in the hunt for a point but failed to produce the goal.