Marco Silva’s upwardly mobile Hornets were good value for a comfortable 2-0 victory, while Saints’ struggles in front of goal continued.
Doucoure pounced shortly before the break from outside the area and Janmaat hit a cracker just four minutes after coming on as a substitute.
Meanwhile, Southampton drew a blank for the third time in their four Premier League matches so far this season.
They have issues to address at the back, too, as there was again no Virgil van Dijk in the line-up.
But instead there was a debut for fellow Dutch centre-back Wesley Hoedt as they continued to be without the club captain.
New boy Hoedt, 23, was kept busy early on by the bustling Hornets striker Andre Gray, while Brazilian youngster Richarlison was proving a handful down the left.
Richarlison created the first decent opening midway through the first half when he evaded two defenders before seeing his shot deflected wide by Jack Stephens.
Neither goalkeeper had been forced into action until seven minutes before half-time when Doucoure latched on to a loose ball outside the Saints penalty area and lashed a right-footed volley past Fraser Forster and into the bottom corner.
Forster denied Richarlison moments later at his near post before Doucoure side-footed narrowly over as Watford finished the half on top.
The Southampton faithful expressed their displeasure with a chorus of boos as the team trudged off at half-time.
Mauricio Pellegrino’s players staged a brief revival after the interval when Sofiane Boufal sliced a shot over and Nathan Redmond hit the side-netting.
Watford’s injury-hit defence was then stretched further when Younes Kaboul and Kiko Femenia both limped off.
But rather than knocking the visitors out of their stride, the changes paid dividends as one of their substitutes, Janmaat, found the far corner from 25 yards out.
Despite the introduction of Shane Long and Charlie Austin, the only cheers from the home crowd were the ironic ones which greeted Southampton’s first shot on target, from Cedric Soares, in stoppage time.
Saints have now failed to find the net in nine of their last 12 league outings Pellegrino said: “It was tough for everybody but we have to keep going and keep working.
“I am here because the team was in trouble last season. If everything was perfect there would be a different manager here.
“In the other games we created a lot of chances and could have won the games. Today was the most difficult game.
“Obviously I’m not happy with our performance.”
In contrast, Watford are flying high with eight points from their opening four matches after producing their third clean sheet in succession.
Hornets boss Silva said: “We deserved three points, we controlled the match which is not easy to do at Southampton.
“I’m really happy with the attitude and the commitment of the players. The first goal was a moment when we worked really hard. And the second goal is a great finish, a moment sometimes you might not expect.”
SOUTHAMPTON: Forster 5; Soares 6, Stephens 5, Hoedt 6, Bertrand 6; Davis 5, Romeu 5; Ward-Prowse 5 (Tadic (46th) 5), Boufal 4 (Austin (71st) 5), Redmond 5; Gabbiadini 5 (Long (69th) 5)WATFORD: Gomes 7; Kiko 5 (Janmaat (62nd) 7), Kaboul 7 (Mariappa (61st) 6), Kabasele 8, Holebas 6; Chalobah 8 Doucoure 9, Carillo 7, Cleverley 7, Richarlison 7; Gray 6 (Deeney 84th)STAR MAN: Abdoulaye DoucoureREF: L ProbertSouthampton’s next game: C Palace, Sept 16 (A)Watford’s next game: Man City, Sept 16 (H)
