The midfielder opened the scoring in the 54th minute by charging down Ryan Schofield's clearance straight into the Terriers' net, after the goalkeeper had reacted far too slowly to a backpass.
Joao Pedro doubled the lead 10 minutes later as the Hornets moved above Reading and into fifth place in the table.
Huddersfield, with almost a whole team sidelined, gave Newcastle loanee Rolando Aarons a full debut.
Just 10 minutes had passed before the game had its first shot of value. Joao Pedro launched the ball from 12 yards after Ismaila Sarr's cross had fallen to him but Schofield dived to parry.
The visitors were fortunate when Sarr won a free-kick that Cleverley lofted on to the head of Adam Masina in the box, but no Hornet had anticipated the knock-down.
Kiko Femenia then scudded a cross from the right across goal as the half continued to lack any quality in the final third.
The Terriers were superior in the passing stakes but Watford's more direct approach saw Schofield rush out to boot away before the pacy Sarr could pounce.
It was not until two minutes before the break that the game's second shot was fired, again at Schofield, who dived to make a similar stop, this time to deny Sarr.
Huddersfield's first shot came in the 53rd minute but Bacuna's 20-yard effort was always on the rise.
Cleverley opened the scoring a minute later thanks to a moment of catastrophic indecision from Schofield.
Alex Vallejo – making his first Championship start – passed the ball gently back to his goalkeeper, who dithered so much that Cleverley was able to charge down the eventual clearance attempt into the net.
Watford doubled the lead through Joao Pedro, who converted Femenia's ball across goal at the back post after Sarr and a defender had both failed to get a touch. It was the teenage Brazilian striker's sixth league goal of the season.