Martin Grainger's whipped-in cross was met by the impressive Rowett to give Birmingham a deserved win in a game devoid of any worthwhile ideas.
Perhaps the suffering home supporters were forewarned, as little more than 8,000 braved the cold weather to witness another lacklustre performance. A set-piece always looked the order of the day.
"The players here are playing as if they're very sorry for themselves," the Watford manager, Graham Taylor, admitted. "It is as if they've got the whole world on their shoulders and they're not showing any signs that they can get out of this run.
"The players have to understand that getting into the Premiership is not the end result but I'm not certain that too many have the self-belief in themselves to see beyond that."
While Taylor pondered his next move, his opposite number, Trevor Francis, was delighted to watch his patched-up troops take a Premiership scalp without fielding a recognised striker within the side.
"It was a determined performance," he admitted. "It was clear that we wouldn't have many chances without a forward in the team and we relied on our quality at set-pieces. There were players fielded out of position all over the place but our endeavour and team spirit saw us through.
"We were without six strikers, two wingers and we lost our regular captain on the day of the game. Only five out of our 16 would have played in a fully-fit team but our desire and application was superb."
Likewise, Watford also fell short in the attacking department, losing their record buy Nordin Wooter with an ankle injury in the opening exchanges while last season's play-off hero Nick Wright made his comeback after a long spell on the sidelines.
A 30-yard curler from Johann Gudmundsson and another long-range effort by Charlie Miller was the sum of Watford's threat, while the visitors remained dangerous with every dead-ball situation. The skill and savvy needed to survive in the Premiership was glaringly absent from Taylor's men, while Francis is hoping for greater things once his injury-ravaged players regain full fitness.
Small consolation for the home fans was the fact that Watford defeated their opponents in the end-of-season lottery seven months ago on their way to a place in the Premiership, a result Francis is unable to forget. "I'd have preferred to win in the play-offs rather than in this Cup tie," he said. But as the winter draws in, it will be Taylor, rather than Francis, worrying about avoiding the drop, while the latter concentrates on learning from his mistakes to make it second time lucky.
Goals: Rowett (66) 0-1.
Watford (4-4-2): Chamberlain; Cox, Page, Palmer, P Robinson; Miller, M Hyde (Brooker 71), R Johnson, Wooter (Gudmundsson 18); Wright (Gibbs 78), Ngonge. Substitutes not used: Williams, Day (gk).
Birmingham City (4-4-2): Poole; Gill (S Robinson 65), Rowett, M Johnson, Charlton; Bass, G Hyde, Holland, Grainger; Purse, Hughes. Substitutes not used: Newton, Dyson, Harrhoff, Bennett (gk).
Referee: P Durkin (Portland).
Bookings: Watford: Johnson, Page.
Man of the match: Rowett.
Attendance: 8,144.Reuse content