Orion Ighalo opened the scoring for the hosts in the 39th minute after Nathan Ake dispossessed Andy Carroll in defence and put in a low cross.
The Nigerian doubled Watford's lead just after the half-time interval, firing home from Ikechi Anya's cut-back.
James Collins was dismissed for West Ham for a foul on Ighalo, as the visitors went down 2-0.
Tomkins has admitted that the Hammers found it tough against Watford.
“They play with two up front, which can be quite a handful,” the 26-year-old told West Ham’s official website. “Not many teams play two up front now, but they were physical and hard to deal with.
“We thought maybe we could dominate in midfield with the numbers we had in there, but we didn’t seem to do that, so that’s another thing…
“They pressed us in numbers and they have good spirit here, which are good things.”
Over the course of the 90 minutes at Vicarage Road, Slaven Bilic’s side had 49% of the possession, took eight shots of which three were on target, and earned two corners.
West Ham are fifth in the Premier League table at the moment with 20 points from 11 matches, just a point behind fourth-place Manchester United.