It looked like Jobi McAnuff's header would be enough for Brendan Rodgers' men until, in the fifth minute of stoppage time, Jon Harley tripped Jermaine Johnson in the area and Jeffers did the rest from 12 yards after referee Andy Woolner had eventually decided to award the spot-kick.
But the official's need to check with his linesman first was symptomatic of an inconsistent display which saw him inexplicably not send Owls skipper Richard Wood off in the closing stages for a clear professional foul on Tamas Priskin.
Wednesday had started the better, but their opening goal after 20 minutes was a gift.
There appeared to be no cause for alarm when Scott Loach went to claim an in-swinging corner from the right, but the Hornets keeper inexplicably let a routine catch squirm through his grasp and Michael Tudgay probably couldn't believe his luck at being presented with the simplest of headers to score his 13th of the season.
Watford may have come into the game as the division's form horse, but they had not really been at the races in the first half until they were the beneficiaries of a truly bizarre equaliser in injury time.
Mark Beevers looked to have a straightforward task in hooking a Harley pass forward clear when it dropped over his shoulder, but, as the defender went to strike the ball, he received a nudge in the back from Priskin, and this may have been a contributory factor in explaining why he proceeded to hammer the ball past stranded Lee Grant.
The Wednesday keeper was picking the ball out of his own net again 11 minutes after the restart.
Tenacious work from Harley ensured a Sean McAllister clearance only reached Don Cowie level with the edge of the Wednesday penalty area on the left and his deep cross picked out McAnuff, who headed back across Grant from six yards to make it 2-1.
That looked like being enough for Watford until Harley's late rash challenge.