But the second half belonged to referee Andy Woolmer.
Brian Laws felt Jobi McAnuff had pushed a defender in the process of heading Watford in front, but the Owls boss had good cause to thank the official later in the second period.
Woolmer amazed everyone by not sending off Wednesday captain Richard Wood three minutes from time when he appeared to commit a professional foul on Tamas Priskin.
And five minutes into injury-time Woolmer needed the intervention of his assistant before awarding a spot-kick after Jon Harley had fouled Jermaine Johnson.
"With referees you take the good and you take the bad," Laws said.
"I had the bad last game against Preston and I'll have to take the good, and I think it was quite fortunate that he decided it was two players coming together (Wood and Priskin), rather than what they call a professional foul.
"That's why he probably only gave a yellow, but I was expecting a red as everyone else was I think."
Watford boss Brendan Rodgers was equally bemused.
Asked if he thought it was a fair result, he replied: "Not when you're in the sixth minute of injury-time and the referee doesn't give a penalty, but his linesman does, then it doesn't seem very fair.
"Tamas Priskin was through one on one. Anyone who's seen Tamas Priskin in the last six weeks will tell you that's a goal, but it's unbelievable.
"How he's produced a yellow I don't know. He wasn't very good.
"But I will look at the positive. Maybe a few months ago that might have been a game we would have lost.
"I think you've seen the fight in the group and some of our play in the second half was very, very good and I just feel for the players that they just didn't get that extra two points which I felt they merited."
Wednesday took the lead in the 20th minute when Loach inexplicably let a routine catch squirm through his grasp and Tudgay had the easiest of finishes.
But Watford got back on terms just before the interval when Beevers fired past his own goalkeeper, possibly as a result of being nudged in the back by Priskin.
Lee Grant was picking the ball out of his net again 11 minutes after the restart.
Tenacious work from Harley ensured a Sean McAllister clearance only reached Don Cowie 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.