The visitors were second best for much of the opening period, with Sebastien Carole going close for Brighton when he crashed a shot against the woodwork.
Brighton went behind when keeper Wayne Henderson tried to clear with a header only for the ball to drop to Eagles, whose lob dropped into the empty net.
And Brighton were unable to find a way past Alec Chamberlain after the break.
Brighton manager Mark McGhee:
"It is to do with our ability to put the ball in the net. All of our good build up play is not turned into good enough chances for our strikers.
"If we can score and win some points we will move out of the relegation zone. We still believe it is possible.
"In this game we had enough chances in the first half, but if you don't take your chances you will lose matches."
Watford manager Adrian Boothroyd:
"I knew it would be hard here, especially after Tuesday.
"It was a big win against a team who work for everything. We looked tired at the start and we weren't at the races.
"The game was too open before the break but we sorted that out and managed to close it out well."
Brighton: Henderson, Mayo, Butters, El-Abd, McShane, Hammond, Carole (Reid 74), Frutos, Gatting (Robinson 79), Hart, Kazim-Richards.
Subs Not Used: Nicolas, Martin, McPhee.
Booked: McShane, Frutos.
Watford: Chamberlain, Stewart (Carlisle 87), Mackay, DeMerit, Doyley, Eagles (Chambers 70), Mahon, Bouazza (Bangura 70), Spring, Young, King.
Subs Not Used: McNamee, Ma-Kalambay.
Booked: Mahon, Young.
Goals: Eagles 45.
Ref: P Crossley (Kent).