The Hornets flew out of the blocks and were firmly in command after 15 minutes, but were unable to build on their two-goal advantage and, by the end of the game, the Owls had reasonable cause to feel hard done by.
After two indifferent performances Aidy Boothroyd would have urged his table-toppers to impose themselves on a Wednesday side, showing six changes from the one that beat Norwich at the weekend. That was exactly what Watford did, scoring with their first attempt after six minutes.
Marcus Tudgay was caught napping as Dan Shittu went past him to flick on Lloyd Doyley's cross and Darius Henderson was not picked up as he stormed into the six-yard area to slam home his sixth goal of the season past Rob Burch.
Wednesday's defence was again at fault nine minutes later when Henderson was held down by Richard Hinds in the penalty area and Marlon King comfortably converted from 12 yards for his third spot-kick success of the campaign.
Watford had their opponents exactly where they wanted them but, instead of seeking to cement the points by the interval, they went into reverse.
The Owls served a warning of what was to come when Hinds' header from a corner was only prevented from going in by a team-mate but, ten minutes before the interval, Brian Laws' men were back in the contest.
Frank Simek crossed from the right, the ball was headed back towards the edge of the penalty area by Tudgay and Graham Kavanagh was given time to pick his spot and he duly cracked a low swerving drive past Mart Poom.
A Henderson header against the outside of the post towards the end of the first half was the closest either side came to scoring again, but although Wednesday looked the more dangerous of the two teams after the break, they were rarely able to threaten Poom's goal.
To add insult to injury for Laws' depleted battlers, they had the lively Jermaine Johnson sent off for a second booking late on.