Ethan Pinnock received a red card for bringing down Ismailla Sarr when in on goal. Deeney made no mistake in dispatching the penalty.
The draw leaves both sides in the play-off places. Watford remain in thrid place and Brentford occupy sixth place.
Story of the match
The pattern of the game became quite clear very early on: Brentford dominated the possession whilst Watford struggled to chase the shadows of the visitors.
Thomas Frank's men came to Vicarage Road and played as though they were at home. Their passing was crisp, confident and purposeful, aiming to create opportunities each time.
The advanced midfield pair of Matthias Jensen and Josh Dasilva ran the show early on. The former played a number of enticing balls in to the box within the opening ten minutes; one tantalising cross narrowly evaded the oncoming Ivan Toney.
DaSilva's link-up play with Bryan Mbuemo on the right-hand side caused issues for Watford. Too many times there was far too much space between the lines which the Brentford duo took advantage of.
And it was in these spaces where Brentford created their first chance. On 17 minutes, Mbuemo found some space to cut onto his left-foot.
He curled a cross towards the back post where Toney was lingering. His movement was perfect; the finish so nearly. His stooped header narrowly flew wide of the far post.
The Championship's top goalscorer was close to finding the net once again on 36 minutes when he rattled the post.
Brentford's build-up play was excellent and Jensen provided the killer pass for Toney before his curling effort from 20 yards hit the frame.
For all of Brentford's domination, they failed to test Ben Foster in Watford's goal in the first half.
Vladmir Ivic would have been foaming at the mouth at half-time, with his side unable to win the ball back, never mind threaten the Brentford goal.
Whatever he said at half-time worked, as the home side looked a different outfit in the second-half.
Captain Troy Deeney finally got touches high up the pitch which allowed the likes of Sarr and Sema to get on the ball as Watford pressed high.
The high press worked wonders for Watford and their hard work paid off just before the hour mark.
The game spun on its head when Ethan Pinnock brought down Ismailla Sarr in the box. A penalty was given and, to make things worse for Brentford, Pinnock was sent off for the challenge.
As he so often is, Troy Deeney was reliable from the spot as he lashed the ball down the middle of the goal. David Raya did stay down the middle, but the sheer power of Deeney's effort put his side 1-0 up.
However, Brentford won a penalty of their own just four minutes later. The instant ripost opportunity was given when Christian Kabasele handled the ball in the box.
Toney cushioned the ball into the bottom right corner and silenced the returning home fans. The finish was drastically different to Deeney's just prior, but the result was the exact same.
Mbuemo did have a chance to put his side in the lead when he latched onto the end of a Dasilva cross. His right-footed effort was skied into the stands from midway in the box.
In an end to end final quarter, Watford had a chance to take the lead when a queue of players attempted to smash home a Ngakia pull-back. Eventually, Tom Cleverley hit it, but Sarr blocked his teammates' shot behind for a goal kick.
With just eight minutes remaining, Watford thought they won the game when substitute Perica found the back of the net following a Sarr cross.
However, the assistant controversially raised his flag to signal offside, despite Perica seemingly in an onside position.
Vladimir Ivic must be feeling some pressure at Vicarage Road. Though results have been favorable and Watford remain in a promotion race, performances have been far from where he would want them to be. It could cause a drop off later in the season.
Boos rang around the ground at half-time after a completely abject display from the home side this evening. Watford must begin to be more proactive and adventurous, especially given the attacking talent in their ranks.
Ivan Toney once again proved his worth to this Brentford side. After losing Ollie Watkins, it was imperative for them to replace his goals adequately.
Toney was the top goalscorer in League One last season, but nobody expected such a fantastic goalscoring record from him so far. He now has 16 goals in 18 appearances for the Bees, which is staggeringly good. His goals yet again prove pivotal to Brentford and Thomas Frank must ensure his side do not become over-reliant on his abilities.