With only 11 league places separating the sides, this was always likely to prove a tricky encounter for Brendan Rodgers' Championship strugglers, but they took the one clear-cut chance that came their way and stood firm at the other end.
There were few scoring opportunities for either side, but the game's decisive moment arrived in the 67th minute when a Jobi McAnuff corner was met by the unmarked Adrian Mariappa.
He headed the ball towards the back post where substitute Grzegorz Rasiak had gambled and duly stabbed home from close range.
That was the Poland international's fourth goal of his season-long loan at Vicarage Road and fully vindicated Rodgers' decision to bring him on eight minutes previously.
The manager received plenty of boos for taking off midfielder John-Joe O'Toole, but the arrival of the forward gave the Iron defence someone other than lone striker Tamas Priskin to think about.
Much of Scunthorpe's pre-match hopes rested on the 27-goal strikeforce of Gary Hooper and Paul Hayes that was reunited following the latter's return from injury.
But the pair met their match in the form of Watford centre-halves Jay DeMerit and Mariappa, who limited their effectiveness and played a major part in ensuring their side kept a second successive clean sheet for the first time since August.
The closest the Iron came to securing a minor upset was arguably with their first attempt on goal, when Martyn Woolford forced Scott Loach into a decent save with a low cross-shot.
The goal apart, Watford mustered only one other on-target attempt which summed up a tie that will not live long in the memory of many who braved the cold to witness it.