Winger Jamal Campbell-Ryce struck early on with a low shot from outside the penalty area and centre-half Lewin Nyatanga doubled the Tykes’ advantage from close-range before the interval.
Striker Jon Macken made sure Barnsley won on home soil for the first time in five attempts with a third five minutes from the end.
Simon Davey steered Barnsley clear of trouble late last season and has repeated the feat with a game to spare.
The FA Cup semi-finalists won successive games on the road after their Wembley heartbreak at the hands of Cardiff, but slumped back into the relegation shake-up with two home defeats.
Barnsley are 17th in the table, while Charlton have slumped to 12th.