Seven wins from their last eight games at Oakwell had helped see the South Yorkshire side move out of the bottom three, but defeat against mid-table Charlton leaves them inside the drop zone, albeit one point behind Blackburn, who are 21st.
Bradley Pritchard gave Charlton a fourth-minute lead, turning home the loose ball after Yann Kormargant's shot had been saved by Luke Steele, before Johnnie Jackson doubled their advantage.
The Addicks exchanged passes on the edge of the Barnsley box before Jackson feigned, causing two home defenders to slide in. The captain took the ball forward before firing a powerful effort between Steele's legs.
Kermorgant headed a third from a superb Rhoys Wiggins cross after 48 minutes and Steele should have kept out Callum Harriott's fourth.
Stephen Dawson was shown a straight red for a lunging tackle on Kermorgant and substitute Salim Kerkar added a fifth as Charlton claimed their ninth away victory of the season to move onto 57 points, six off the play-off places.
Good hold-up play by Ricardo Fuller brought in the substitute who thundered an effort past Steele.
A horrible day for the home side was capped by a second sending off when Tom Kennedy brought down Fuller when last man. And it was Fuller who curled in a sixth in stoppage time.