The teams started the match with identical records and the same points just above the drop-zone but the Yorkshiremen gained their second away victory in five days and their first ever at The Valley with consummate ease.
The patient home crowd, who have now seen their side win just once in nine games, called for the head of beleaguered boss Alan Pardew.
Barnsley, who had previously only scored two goals away from home this season, were three goals in front by half-time after an inept display by the home side who were bereft of confidence.
Pardew once again tinkered with the team, making three changes from the side that drew in midweek with Ipswich Town.
All three of Barnsley's goals came from set-pieces. It took just three minutes for the visitors to stun the home side when Charlton failed to clear Iain Hume's free-kick and Jon Macken rifled the ball into the net from 15 yards.
Lloyd Sam missed a good chance for Charlton and Andy Gray toe-poked an effort wide before Macken scored a second on 17 minutes, netting after goalkeeper Nicky Weaver could only parry away Anderson de Silva's effort.
Charlton's embarrassment was compounded on 39 minutes when Robert Kozluk's free-kick was met by an unmarked Darren Moore who looped a header into the Charlton net - his first goal for Barnsley.
Charlton improved marginally in the second half but the damage was done and they faced a lost cause although they did pull a goal back when skipper Mark Hudson headed home Grant Basey's 75th-minute free-kick.
There were more boos and cat-calls for Pardew to be sacked at the final whistle and a number of supporters protested outside the directors' boardroom as the former Charlton player's future hung in the balance.