Lee appeared to dive too far across his goal when Addicks winger Darren Ambrose let fly from the edge of the area and his shot slipped through his grasp and into the net.
Nathan Ellington's first goal for the club since his club record £3.75million move from West Brom in the summer had looked to be enough to secure Watford's first home win since late October before Ambrose's speculative late strike was fumbled in.
Ellington was handed a rare start in place of Marlon King - whose £5million move to Premier League strugglers Fulham remains ongoing - but was anonymous until latching on to Darius Henderson's pass to stroke home.
Both sides struggled to string together a passing move of any note in a forgettable match played out in testing conditions and the loudest cheer of the afternoon was reserved for the arrival as a sub of midfielder Al Bangura.
Bangura was this week finally granted a work permit to remain in the United Kingdom and despite not being fully fit after an ankle injury took his place for a late cameo.
The Hornets held a nine-point lead at the top of the Championship at one stage of the season but started the match in fourth place after a dire run of form.
And without the threat and presence of King in attack Boothroyd's side served up even less of a spectacle than normal in a drab affair.
Jay DeMerit flashed a header wide from Jordan Stewart's free-kick before Damien Francis shot over after Jobi McAnuff headed back across goal in the opening exchanges before Lloyd Sam wasted a good chance to give the visitors the lead on the half hour mark.
A goal kick was flicked on by Luke Varney and Sam broke in behind debutant Calum Davenport but slashed his left-footed shot high and wide.
A rare piece of quality then saw Ambrose pick out Chris Iwelumo at the far post but his header drifted over before Ambrose then missed a sitter.
Matt Holland broke clear down the right and at full stretch cut a fine cross across the area.
Ambrose was in oceans of space with just Lee to beat but horribly scuffed his effort wide of the far post. The second half started in equally poor fashion before Ambrose forced Lee into a save with another effort from outside the box before Sam latched on to Zheng Zhi's poor touch to rifle a strike narrowly past the post.
Alan Pardew's side were piling forward in search of a goal but fell behind to a soft goal in the 59th minute.
Stewart's long free-kick was controlled by Henderson and he chipped it into the box looking for the run of Francis.
The ball ran behind the midfielder but found Ellington unmarked and he coolly steered home from 12 yards.
Watford looked like holding on to a valuable win before Ambrose again let fly from range in the 78th minute and Lee's error saw the ball end up in the back of the net.
Any reproduction, publication or redistribution of this material without the written agreement of 365 Media Group is strictly forbidden.