Newcomer Carl Robinson made an immediate impact, but it was substitute Pedro Matias who eventually eased Walsall to their welcome win when he carved out the vital second half goal for Jorge Leitao.
Watford often promised to take command but lacked finishing touch to take advantage of Walsall's injury problems.
There was an early casualty when a linesman limped out of the game after only nine minutes with a leg strain. Nine minutes later Walsall's central defender, Danny Hay, damaged his shoulder and was replaced by Matt Carbon.
Watford operated more smoothly than the Saddlers in the early stages and only a good save from Jimmy Walker from Heidar Helguson kept the home side in the game.
The dramatic turning point occurred in the 25th minute at a time when Watford were moving into top gear.
Darren Bazeley produced an innocuous cross from the right which floated on to the angle of the crossbar and bounced to David Zdrilic who headed the ball back into the middle for Junior to head home.
Watford then found themselves under pressure and they were indebted to Marcus Gayle. He kept out a Robinson header with goalkeeper Alec Chamberlain well beaten.
Junior, however, blotted his copybook when he was needlessly booked for an infringement when he blocked a free-kick.
Newcomer Jason Norville produced some pleasing touches. The nippy teenager was often a big threat but the Saddlers survived to maintain their first-half lead.
But it was only after Norville was replaced by Gifton Noel-Williams that Watford found their attacking flair.
Stephan Glass set up Helguson with a perfect pass but Walker spotted the danger and blocked the striker's shot.
Walsall then suffered the loss of Carbon with double vision as the Saddlers battled to maintain their slender advantage.
But Zdrilic should have sealed the game when the Australian headed a cross from Matias wide of a gaping net.
In the following minute in a repeat situation, Zdrilic saw his header well saved by Chamberlain.
Matias continued to torment Watford and in the 86th minute raced away down the left to produce a cross which Leitao headed home to give Walsall their vital win with his eleventh goal of the season.