Gianfranco Zola's side responded well and Deeney went close twice before the equaliser finally arrived.
It was Watford's 1,000th draw in league football and sees them slip to ninth while Charlton remain 17th with just five points.
Watford manager Gianfranco Zola:
"The expectations were different for today's match and things didn't go the way we wanted. But it is a good point considering we went down and it wasn't easy, so I take it as a positive thing.
"There are obviously a lot of things that didn't work as I wanted and I know exactly what those things are and we're going to be addressing them tomorrow and working a little bit on that."
Charlton boss Chris Powell:
"It's a tough place to come, a decent team and we had the victory in our last game and we wanted to build on it.
"Obviously taking the lead, you want to try and see it out and try and take three points but I think it was a well earned away point.
"It was quite a heated battle at times but of course it was definitely a penalty. They obviously got their equaliser, it was a little bit nip and tuck and they put us under pressure towards the end but our players stood up to it."
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