Hornets striker Troy Deeney was involved in all of the home side's best moves in the first half, firing wide after rounding goalkeeper Alex Smithies and striking the Huddersfield crossbar before slotting home a penalty just before the break.
Vydra was fouled for that spot-kick and he doubled his side's lead shortly after the interval before grabbing his second of the afternoon from a Deeney assist in the 74th minute.
Cristian Battocchio rounded off a comfortable win with five minutes left, flicking the ball into the far corner after a fantastic passing move.
Craig Forsyth had the first chance of the match, forcing Alex Smithies into a save in the sixth minute from the centre of the penalty area as the Hornets started brightly.
The visitors, without an npower Championship win in 11 games, threatened for the first time six minutes later with winger Sean Scannell firing a snap shot wide from 20 yards.
Watford came into the match having scored 49 times during an impressive first half of the league season and they went close to number 50 seconds later when striker Deeney ran clear but he missed the target from a tight angle after rounding Smithies.
Huddersfield's strike duo of former Everton forwards Jermaine Beckford and James Vaughan kept the Watford defence on their toes and combined in the 20th minute but the latter fired straight at goalkeeper Manuel Almunia.
Vaughan was then inches away from connecting with Scannell's driven ball and Nathaniel Chalobah shot wide at the other end.
Two minutes before the break the home side went incredibly close to breaking the deadlock, with Deeney's curling effort hitting the bar before defender Peter Clarke, making his 150th league start for the club, cleared the former Walsall's men close-range effort on the line.
Marco Cassetti drove wide at the end of a flowing move before Deeney opened the scoring from the spot just prior to the half-time whistle after Calum Woods halted Vydra's run.
Zola's men doubled their lead after 57 minutes when Vydra stretched to meet an inviting cross from Cassetti with an effort that Smithies could only push into the roof of the net.
Former Arsenal man Almunia had been well protected by his defence during the opening hour but was forced into a stunning one-handed save to deny Beckford in the 63rd minute as the Terriers looked to get back into the match.
The 673 travelling fans were starting to believe they could do just that before Vydra put the game to bed with 16 minutes to go, slotting home after being put through by Deeney.
Cristian Battocchio then put the icing on the cake in the 85th minute, meeting Cassetti's cross with a lovely flick into the back of the net with the outside of his boot.