A deflected Tommie Hoban header from a right-wing corner gave Watford the lead before a perfectly weighted through ball from Dale Stephens enabled Ricardo Fuller to equalise for Charlton.
The visitors were reduced to ten men at the end of the first half when Fernando Forestieri received a second yellow card for simulation.
The Addicks were on the front foot in the second half but conceded an unnecessary free-kick twenty minutes from time. Swiss international, Almen Abdi, curled home a terrific strike to seal a 2-1 win for the Hornets.
Charlton have now taken just two points from twelve in their last four games at The Valley. It is a statistic they need to improve very quickly, particularly with three difficult away games coming up this month.