The Lions also had Danny Dichio sent off after receiving two bookings.
The Hornets nearly stole the lead in the 13th minute when Brynjar Gunnarsson connected with Paul Mayo's cross. His powerful header left Graham Stack rooted to the spot, but the Icelander saw his effort hit the underside of the bar. The ball then bounced down on to the goalline before it was hacked away to safety.
Despite appeals from the Watford players, referee Paul Taylor adjudged that the ball had not crossed the line.
Gunnarsson's miss prompted a swift reply from the Lions as Barry Cogan looked to stamp his mark on the game. He first burst through the Watford defence before unleashing a right footed-shot that was deflected wide of the post by ex-Millwall defender, Sean Dyche.
From the resulting corner, Cogan looked to have given Millwall the lead when he converted Peter Sweeney's corner sending the ball into the roof of the net. But the midfielder's celebrations were cut short by Mr Taylor, who ruled that Dichio had impeded Richard Lee in the Watford goal.
The Hornets then took the lead in the 65th minute with a well-worked goal. Neal Ardley drifted out on to the left wing before laying the ball off for Neil Cox.
His cross was met by the head of Helguson, Stack could only parry his effort, leaving Webber with the simplest of tap-ins at the far post for his ninth goal of the season.
Millwall's cause was then not helped when they had Dichio sent off after receiving a second booking after he left Watford's Mayo in a heap on the floor following a late challenge.
Ten-man Millwall could not contain the Hornets as Helguson added a second 11 minutes later.
The striker raced on to a long ball before releasing a low shot that nestled in the bottom right corner of Stack's net after Kevin Muscat had given the striker too much room.