The Czech striker took his tally for the season to 12 goals with two in the space of two second-half minutes to shoot down the Seagulls.
Brighton boss Gus Poyet was going head-to-head with his old Chelsea team-mate, Watford chief Gianfranco Zola, but a dour first half in the pouring rain left both sets of fans feeling the Blues.
However, the game came to life after the break when Troy Deeney grabbed his 50th career goal and David Lopez equalised for Brighton with a penalty before Vydra had the final word.
Watford could have gone ahead at the beginning and the end of that scrappy opening period.
Daniel Pudil gave Wayne Bridge the slip from Almen Abdi's early corner but put a free header over the crossbar.
And in stoppage time Albi's deep cross was met by Deeney but, once again, the striker could not get his header on target.
Mercifully, the second half was a far more entertaining affair with Watford breaking the deadlock after nine minutes.
Pudil's diagonal ball played in Deeney, who had peeled off his marker Adam El-Abd, and his low shot was powerful enough to fizz through Kuszczak's legs via his heel and into the back of the net.
But out of almost nothing Brighton managed to hit back 10 minutes later.
Kazenga LuaLua had been forced away from goal and towards the corner of the penalty area by Manuel Almunia, but Tommie Hoban saw fit to barge the winger over and referee Oliver Langford pointed to the spot.
Spaniard Lopez stepped up to score his second penalty in as many matches.
But Brighton were level for barely two minutes before Watford got a big slice of fortune.
Vydra was allowed to run unchecked towards the Brighton area but his shot took a huge deflection of El-Abd to loop over Kuszczak and into the net.
However, there was nothing lucky about Watford's third goal a minute later as Deeney, inside his own half, lifted the ball into the path of Vydra who outstripped the Brighton defence before coolly beating Kuszczak.