Lewington rested six first teamers with one eye on Sunday's FA Cup quarter-final tie against Burnley at Vicarage Road.
The Hornet's much weakened side and referee Ross left them even more depleted when he showed skipper Sean Dyche a red card after 29 minutes.
By then Preston were ahead when Graham Alexander fired home from the penalty spot after 19 minutes.
Dyche had been the offender then, pulling Richard Cresswell's shirt in the penalty area. The referee pointed to the spot, Preston scored but the home captain continued to complain about the decision and was duly booked.
Twelve minutes later Jonathan Gould caught a dropping ball in the box only for Dyche to come in with a late challenge to fell him. A melee ensued after which referee Ross showed Dyche a second yellow card.
"The referee had no option. It was a rash challenge and not typical of the player," said Lewington after the game.
Watford set about trying to retrieve the deficit in workmanlike fashion but it was a scrappy game.
After the break Watford keeper Richard Lee, making his debut, tipped over the crossbar a shot from Marlon Broomes.
Back came Watford with Gifton Noel Williams sending in a header which keeper Gould managed to pluck out from beneath the crossbar.
Watford rang the changes but after 80 minutes Richard Cresswell had a great chance of easing Preston's anxiety when he broke from deep inside his own half and ran 60 yards unchallenged only to blaze over the bar with just the keeper to beat.
Preston boss Craig Brown admitted: "We stole three points from Watford under cover of darkness tonight.
"The referee is one we've had before and I thought he was a good one. But the decisions got the crowd behind Watford and made it harder for us."
Lewington was unrepentant at making six changes to the first team that drew at home to Nottingham Forest on Saturday, claiming: "Weighing this match against the quarter final it is important that we avoid any injuries because Sunday's game is the most important of the season.
"You don't often get a chance as a First Division club to reach the semi finals."