A Victor Lindelöf own goal, a Maxim De Cuyper strike and a Jack Hinshelwood double put Brighton out of sight inside the first half-hour, before Gomes' dismissal for kicking out at Georginio Rutter completed a miserable afternoon for Unai Emery's side.
Emery, speaking to Match of the Day, said the damage was done once the game's first mistake was punished.
"We started good in the first 10-15 minutes. When we made the first mistake, they scored and then we lost our balance emotionally and we conceded three more goals. It was a tough moment and with the red card was more difficult. The only good news for me was how the players responded in the second half."
On Gomes' dismissal: "Maybe the first yellow card was not fair, but OK. We must accept."
Asked whether it had been his own decision to leave Watkins out of the squad, Emery declined to elaborate.
"This question is for him. You can call him and try to get his answer. The players here wanted to play and we had two strikers with a small injury."
Speaking later, Emery reflected further on a chastening opening 25 minutes.
"Tough match, tough 20-25 minutes. Mistakes, and again we are building the team, and building the team, we can make some mistakes. Today we were so, so unlucky, because each mistake we made, they were scoring. We conceded four goals in the first half – it was a crazy moment."
He praised the response after Gomes' sending-off, "The second half, I think the players responded fantastic. We tried to get a new plan in the dressing room, playing the second half like we did without one player, trying to be always not losing our mind, being as well focused in our gameplan and trying to avoid conceding more goals or chances like we did."
Looking ahead to next Monday's trip to face Arsenal, Emery pointed to Aston Villa's history of overcoming slow starts.
"Of course, we have some circumstances, they are not helping us, but those circumstances we had before as well, last year, two years ago, three years ago, and always, we overcame it. And this is now the new objective as well; try to finish the transfer window and start with the players we will have.
"Of course, in Premier League, 38 matches, each point is very important, but today we lost three, and now the next match is next Monday against Arsenal at home. Hopefully, in Villa Park, we can feel stronger and more comfortable and more confident."
Brighton boss Fabian Hürzeler, also speaking to Match of the Day, said his side's pressing had forced the errors that shaped the game.
"We had a tough start but afterwards we got the control back, we pressed intensely, we forced them to do mistakes so it was quite positive. In the end the red card was a game changer."
On managing a 4-0 lead at the break, he added: "We still had a few chances and wanted to score but the clean sheet was very important."
Hürzeler credited his side's rhythm in the first half.
"We were effective out of possession. We were there in the right moment. We got into a flow and when you are in a flow a lot of things can happen. We have to stay humble, keep working hard because on Thursday we have the next challenge."
He also praised Brighton's younger players: "We need every player. We will always get young players in full of potential, it's up to us to develop them. It was a positive start so let's keep pushing them."