Goalkeeper Adam Davies and Kenny Dougall returned from international duty and Dani Pinillos reclaimed a starting position after injury.
It proved to no avail as the counter-attacking plan set out by Charlton coach Lee Bowyer sent the Reds to just their second league defeat of the season.
“That’s our best performance,” he said. “They’re the best side we’ve played so far but as good as they are in possession, you can hurt them on the turnover. That was our plan.”
Karlan Grant scored twice, taking his league tally to seven, and his pace troubled Barnsley throughout.
Barnsley came into the match as the second-highest scorers in League One but, despite plenty of possession, they struggled to threaten.
Grant opened the scoring after eight minutes, taking a super diagonal pass from Jamie Ward and hitting a low shot across Davies and in off the far post.
Alex Mowatt forced a diving save from Jed Steer from a long-range free-kick after 16 minutes, but that was the only time Barnsley threatened in the first half.
In contrast, the speedy Charlton forwards kept the Tykes’ defenders at full stretch and Ward twice had shots saved by Davies.
Barnsley introduced top scorer Kieffer Moore at half-time but to little effect and Charlton struck seven minutes into the second half as Grant converted Lyle Taylor’s low cross from close range.
Charlton Athletic: Steer, Dijksteel, Bielik (Sarr 82), Pearce, Solly, Cullen, Reeves (Lapslie 74), Aribo, Ward (Fosu 62), Taylor, Ahearne-Grant. Unused substitutes: Phillips, Marshall, Pratley, Ajose.
Barnsley: Davies, Cavare, Pinnock, Lindsay, Pinillos (Hedges 60), Dougall, Mowatt, Potts, McGeehan (Moore 46), Moncur (Thiam 60), Brown. Unused substitutes: Walton, Jackson, Ben Williams, Adeboyejo.
Referee: J Linington (Isle of Wight).