Nani prodded the ball home after the Spurs goalkeeper placed the ball on the ground feeling a free-kick had been awarded by Clattenburg for a handball by the United player.
The referee allowed the goal to stand, though, seemingly having invited Tottenham to play on, and United went on to claim a 2-0 win at Old Trafford.
Gomes said: "In my opinion, the whole stadium saw what happened. It is impossible the ref did not see the handball.
"He did not gesture in any way to play on, like you would normally expect. When I put the ball down on the floor, he started gesturing with his shoulders.
"He is supposed to use his hands. It was not clear to anyone. It was only when I saw Scholes shouting at Nani to shoot that I reacted.
"The biggest mistake was not being clear afterwards. Maybe he did not have to give the foul but you have to be clear. He only gestured after I put the ball down.
"Nani stopped the game with his hands but this is not basketball."
Gomes maintains that, as far as he is concerned, he did nothing wrong.
He added in The Sun: "I feel bad, as I let in a goal. But I would react the same again.
"The ref was not clear. He gesticulated with his shoulders and barely moved his arms. He was not able to explain and show to anyone in the stadium what was going on.
"Even the linesman was confused. He told me he did not know what the ref gave.
"He said he saw the handball and told me to go back to the goal, that he would tell the ref what he saw."