Millwall were reduced to ten men in the 53rd minute after Danny Dichio was shown a second yellow card after catching Watford skipper Sean Dyche across the bridge of the nose with his elbow.
Dyche received treatment while Brighton official Clive Penton showed Dichio red.
The Millwall striker had been sent off again Watford earlier this season for two yellow cards and picked up his first in this match after 31 minutes when he kicked out at the former Millwall stopper Dyche.
The Millwall management team were less than happy with the decision, but it proved to be the turning point.
The Lions had the better of the opening exchanges with Marvin Elliott seeing a powerful drive tipped just wide by keeper Paul Jones. Then Barry Hayles glanced a header just beyond the post.
Watford came through strongly after 20 minutes. Heidar Helguson headed just over and then James Chambers raced in to turn a shot beyond keeper Andy Marshall, but inches wide of the far post.
Then Helguson climbed to meet a Neil Cox free-kick, but Marshall tipped the effort over the bar.
Millwall again started the second half exerting pressure but this understandably fell away when they were reduced to ten men.
Watford began to build up a head of steam. Jermaine Darlington saw his shot deflected over the bar and Brynjar Gunnarsson had a close-range header blocked by the keeper, then Helguson's header seemed set to find the net only for Marcus Phillips to deflect it wide.
The breakthrough came on 74 minutes with Helguson touching in an inspired pass from Anthony McNamee.
Watford were hanging on in the end with Alan Dunne heading against the bar and Josh Simpson following up with an attempt which clipped the post.