The match ended in a goalless stalemate even though both sides created plenty of chances, but Arsenal, reduced to 10 men when Emmanuel Eboue was sent off after 36 minutes, had the ball in the net in the 15th minute when Eboue thought he had scored.
"It was a regular goal," Wenger told reporters, "and I think it was two points dropped. The goal was cancelled because the referee saw an illusionary foul. I have seen it three times on television and I still don't see what was wrong.
"He saw a push from Eboue, but in fact it was (Jonathan) Woodgate who stumbled over (Emmanuel) Adebayor and fell down. It is not acceptable. I am not against the referee, but he got a big decision wrong."
It was an eventful afternoon for Eboue who was first booked for dissent soon after the goal was scored and then sent off for a retaliatory kick at Tottenham's playmaker Luka Modric.
Regarding Eboue's dismissal, Wenger said: "...if he retaliated he deserved a red card and it will be dealt with."
Eboue later apologised for his red card.
"I am sorry," he told Arsenal's website. "This game was very, very important for us. We must always win when we play against Tottenham and give our best for the fans.
"I know have to control myself [on the pitch] but I did not want to let Tottenham win."
Although the result increased Arsenal's unbeaten run to 11 matches in all competitions, seven of which they have drawn, it left them in fifth place, five points behind Chelsea who occupy fourth spot in the race for Champions League berths.
Tottenham manager Harry Redknapp also thought the result represented two dropped points for his side in their battle against relegation. Spurs are 15th, just two points above the relegation places.
"We dominated them when it was 11 v 11 and we dominated them when they were down to 10 men, even though they made it very hard for us and they were difficult to break down," he said.
