The Reds competed well in the first half and could have scored through a Marcus Tudgay header while Emile Sinclair's effort was cleared off the line.
Gianfranco Zola's Watford, who shot into the play-offs after this win, had an incredible 24 shots throughout the game and had it not been for the woodwork, which they hit three times, and the brilliant Luke Steele, the scoreline could have gone into double figures.
The Hornets took the lead in the first half as Troy Denney headed in a corner. They doubled their advantage after the break when Martin Cranie allowed Mark Yeates space on the left hand side and the winger slotted past Steele.
The third came in bizarre fashion as Cranie hacked down the lively Fernando Forestieri and as the former Coventry man argued with the referee, Forestieri took a quick free-kick and Deeney smashed home from just outside the box.
The fourth was equally calamatous from a Barnsley point of view as Jim McNulty fouled Matej Vydra and the Czech striker slotted home from the spot.
The Reds pulled one back in the last minute through Marcus Tudgay but it was too little too late for Barnsley who are dangerously close to the Championship's drop zone.
