Watford scored five times after the break with Deeney opening his account 11 minutes into the second half before adding his second two minutes from full-time.
The striker then completed his, and the Hornets' scoring, with an injury-time penalty to become the first Watford player since Michael Chopra in 2003 to score a hat-trick.
The Cherries were well in the contest at the break with the score at 1-1 but after scoring two quick-fire goals within the first 15 minutes of the restart, last season's beaten play-off finalists took complete control.
Both sides traded early attempts before Watford scored their first home goal of the season in the 13th minute.
After an Ikechi Anya shot had been deflected behind, Almen Abdi's right-sided corner was allowed to bounce in the heart of the penalty area.
Deeney looked to be having his shirt pulled but he did well to hold off an opponent and the ball broke invitingly for Gabriele Angella to fire into the roof of the net to score his second in as many games following his arrival from Udinese in the summer.
Bournemouth, who came into the game defending an 11-game unbeaten run in all competitions, battled back well with Lewis Grabban forcing Manuel Almunia to block an angled drive behind with his legs before hitting a shot against a team-mate from the resultant corner.
The Cherries continued to control the middle passage of the first half and it was no surprise when they equalised in the 29th minute when Ryan Fraser was found in space on the right side of the penalty area and his low cross was tapped home from close range by Grabban, who had scored both his side's goals in their opening day win over Charlton.
Bournemouth's disciplined approach had broadly coped well with Watford's array of attacking talents in the first half but within ten minutes of the restart the contest was effectively over.
Like their first goal, the Hornets' second was from a set piece, although this time a free-kick, but again it was the same combination that worked to positive effect as Angella rose highest to head in Abdi's delivery from the left in the 52nd minute.
Unlike their first goal though, Watford were able to follow it up with another one soon after as in the 55th minute Fernando Forestieri and Deeney combined superbly before the former slid in the latter and his angled finish was deflected beyond the reach of Ryan Allsop.
The Hornets were now in the groove and they made it 4-1 in the 66th minute when Iriney won the ball in the centre of the park and found Abdi, who advanced before sliding the ball forward to his right and McGugan kept his composure to pass it beyond Allsop to net his first goal since moving from Nottingham Forest in the summer.
That looked increasingly like it would be the end of the scoring until two minutes from time when Deeney did very well to create a shooting opportunity before rifling a drive past Allsop from the edge of the penalty area.
And there was still time for Deeney to complete his hat-trick when he converted an injury-time penalty after Diego Fabbrini had been tripped in the area.