Saints' top scorer Rickie Lambert bagged all three goals as the South Coast club also extended their unbeaten run to six games at Vicarage Road.
After an even start to the affair, Lambert was gifted his first on 13 minutes after on-loan Manchester United keeper Tomasz Kuszczak failed to reach a cross which Lambert headed home.
The lead was doubled nine minutes later, when the visitors took full advantage of a misplaced Nyron Nosworthy pass.
Adam Lallana capitalised and squared the ball to Lambert, who fired a low, unstoppable shot past Kuszczak.
The visitors continued their dominance after the interval and Lambert sealed the points by completing his treble from the spot after Tadanari Lee was tripped in the area.
Nigel Adkins's men are now one point clear of West Ham but have played a game more while Watford remain 17th.