In the 22nd minute, Daniel Pudil skipped away from his man and picked out McGugan at the near post to make it 2-0.
However, Troy Deeney extinguished any lingering hopes of an Owls comeback within four minutes of the restart when he raced away from a flat-footed home defence and kept his cool to slot the ball beyond Kirkland.
Deeney grabbed his second of the afternoon - and his 20th of the season - just a minute later when he tapped home after Mathias Ranegie's strike had bounced back off the post and fell kindly at his feet.
Afobe reduced the arrears three minutes later with a neat header to cap off an exciting 10 minutes immediately after the break, but Watford held on to secure all three points. body check tags ::