The home side went into the game without a victory in 10 matches and having lost five successive games at Vicarage Road.
Lomas said: "We came with a game plan. Obviously Watford hadn't won in quite a while so we wanted to come and quieten the crowd.
"The last thing we wanted is a start like that and to concede a penalty and to get a man sent off. It was absolutely catastrophic.
"Obviously we knew it was going to be a long day after that. Steve Morison's had a chance to make it 1-1 but once the second goes in you know it's going to be a long, long day."
The Millwall fans chanted for Lomas to lose his job at various stages of the game but he added: "I always knew the situation. The buck stops with me, I'm the manager, simple as that, but we've just got to get on with it.
"We've got another game in two days, we've got to regroup, see who's fit and try and put in a performance that shows the fans the players are fighting for them as much as me."