Watford, who were given hope after Hull's dramatic draw with Cardiff, needed just a win over Leeds to secure Premier League promotion after the first half saw a stoppage of 16 minutes following goalkeeper Jonathan Bond's serious injury.
Bond was stretchered off after Dominic Poleon's push into the back of Ikechi Anya caused a huge collision, meaning that third choice goalkeeper Jack Bonham made his debut.
And it was Bonham's mistake that led Leeds to victory, after Watford pushed for a late winner and Ross McCormack hit the Hornets on the break, lobbing over the 19-year old.
Bond, who was taken to hospital in the first half after Poleon's shove to Anya, was only on the pitch after regular keeper Manuel Almunia injured himself during the warm-up.
To add insult to injury it was Poleon, himself on as a sub for the injured Steve Morison, who put Leeds ahead.
In the 42nd minute Poleon again chased a long ball over the top into the area.
This time the striker checked his run, Joel Ekstrand's clearance hit him in the chest and as defender and goalkeeper collided, Poleon nipped in behind to tap the loose ball into an empty net.
But the Hornets hit back during no less than 16 minutes of time added on at the end of the first half.
Anya made a surging run across the penalty area and played the ball to Almen Abdi, who curled in a superb first-time shot from the edge of the area for his 12th goal of the season.
Things got worse for Gianfranco Zola's side when they lost Deeney to a second yellow card in the 60th minute for a foul on Michael Brown.
However, the 10 men battled on and midway through the second half substitute Matej Vydra brought a fine diving save from Paddy Kenny.
Then came news of the dramatic events at the KC Stadium and Watford, who now knew a win would secure promotion, suddenly had a spring in their step.
Kenny saved from Nathaniel Chalobah and Fernando Forestieri as they piled forward looking for the winner.
But instead a minute from time McCormack was put clear at the other end and chipped the stranded Bonham who could only fingertip the ball up and over the line to condemn Watford to the play-offs.