After a first-half stalemate, the Tykes went ahead 55 minutes with a spectacular strike from Icelandic midfielder Emil Hallfredsson, but the home side finished with ten men after Ryan Shotton was sent off.
Buoyed by the impressive midweek victory at Preston, Mark Robins named the same side to face a Watford outfit who had a comfortable win over high-flying Sheffield United.
With Andy Gray the lone striker for the Oakwell side and Brazilian midfielder Anderson de Silva patrolling just behind, the home side produced a couple of early threats.
Filipe Teixeira, on loan from West Brom, was heavily involved down the Barnsley right and did well to produce an early shot after good work by Hallfredsson.
Hallfredsson went close when he smashed a shot just wide from the edge of the area as Scott Loach back-pedalled after being stranded at the edge of the box.
On the break Lloyd Doyley pushed forward down the left and slotted an inch-perfect pass inside and Jon Harley should have done better, but dragged his shot wide.
A sweeping move forward came close to breaking the deadlock but Gray was shut out after Hallfredsson's super cross from the left and then Teixeira's shot went wide.
Watford saw half hearted appeals for a penalty turned down when Henri Lansbury crashed down in the box under a challenge from Darren Moore.
Early in the second half Barnsley manager Mark Robins decided on a change taking off de Silva for Jay Rodriguez, on loan from Burnley.
A minute later the home side were in front when Hallfredsson latched on to Gray's pass flicked the ball past Adrian Mariappa and smashed a super shot beyond Loach.
Barnsley were hampered for the last 13 minutes after a rash lunging tackle from Shotton that brought him a straight red card.
It set up a hectic finish as the Hornets hurled everything forward looking for an equaliser.
Barnsley keeper Luke Steele made a brilliant late save to preserve the points when Lansbury hit a super free-kick.