Watford have now gone four Championship games without a win after they had to come from behind to earn a point at home to Charlton.
Kermorgant fired the visitors in front from the penalty spot a minute after the restart but a draw was the least the Hornets deserved and it was Pudil who secured it with a goal 20 minutes from time.
Gianfranco Zola tweaked Watford's formation for this game, moving from 3-5-2 to 3-4-2-1, and it initially caused problems for the visitors.
Fernando Forestieri twice found space in the opening minutes, first seeing a shot blocked before going much closer when he fired across keeper Ben Hamer and narrowly wide of his far post.
The Hornets looked as if they could be a threat on the counter-attack but, with the extra man in a five-man midfield, Charlton looked the more comfortable side as the opening half progressed.
Zola's side did threaten to open their opponents up when a Gabriele Angella interception gave Diego Fabbrini the opportunity to run at the defence before releasing Forestieri.
Once again, however, he was unable to hit the target with a shot.
Charlton did have the ball in the net soon after when Richard Wood bundled the ball over the line after Manuel Almunia had blocked a Dorian Dervite header on the line, following a free-kick but the assistant's flag was already up for offside.
Temperatures increased around the half-hour mark when Essaid Belkalem tripped Simon Church on the edge of the penalty area.
Although Johnnie Jackson's free-kick hit the wall and span behind for a corner, that set-piece saw Marco Davide Faraoni and Church get involved in a scuffle as the ball was played into the 18-yard box and ended with both players getting booked.
But it was the visitors who broke the deadlock soon after the restart when Belkalem's unnecessary sliding challenge brought down Lawrie Wilson in the penalty area, and Kermorgant duly dispatched the spot-kick high to Almunia's right to make it 1-0.
The Hornets responded to that setback positively and twice could have equalised in the next 10 minutes.
First Hamer made a good parrying save to keep out a well-struck Deeney shot, and then the striker's cushioned header set up Lewis McGugan, but he fired wide of the target when well placed.
Deeney went close with a powerful 25-yard effort before Watford's pressure was rewarded in the 70th minute when Hamer could only parry a well-struck Fabbrini shot back into the heart of the penalty area, and Pudil tucked away the rebound.
While the momentum was with the home side in the closing stages, it was Charlton who could have snatched the win when Rhoys Wiggins' low centre from the left was latched on to by Jackson, but he could not hit the target.
However, McGugan went closer still for the home side when he fired a 25-yard effort just the wrong side of the Hamer's right-hand post.
But what was arguably the best chance of all came two minutes into stoppage time when Scotland's new hero Ikechi Anya showed great pace down the right before pulling the ball back to Deeney, but he lifted a shot over the bar from close range.