Watford fashioned their first real chance in first-half stoppage time after Femenia motored across the pitch and crossed from the left, with Richarlison’s header clipping the crossbar.
Injuries bit for both teams in the second half, Matic hobbling off for United, to be replaced by Ander Herrera, and Watford’s Will Hughes giving way for Roberto Pereyra after injuring his hamstring.
Watford head coach Marco Silva also sent on midfielder Andre Carrillo, shifting to a back four, and his side began to look more dangerous, Richarlison heading wide from another Femenia cross.
There was a further lift for the home fans when Deeney made his return after a three-game suspension.
United squandered several chances to extend their lead, with Lukaku the chief culprit, twice shooting wide and then dawdling over a chance made by Pogba, enabling Adrian Mariappa to get back and block.
Deeney reduced the arrears with 13 minutes left, sending David de Gea the wrong way from the spot after a rash foul on Pereyra by Marcos Rojo.
Doucoure made it 3-2 with six minutes remaining, neatly stabbing in Carrillo’s cross, but Lingard killed off Watford’s comeback hopes with a brilliant 70-yard run and an assured low finish past Gomes.