Alli was hit on the side of the head in the 73rd minute by a plastic bottle thrown from the stands.
He then gestured the 2-0 scoreline to the crowd, before being led away by Spurs captain Harry Kane.
Arsenal are analysing CCTV in a bid to identify who threw the bottle at Alli.
Speaking to Sky Sports after the game, Alli appeared unfazed by the incident, saying it made his goal “sweeter”.
On Twitter after the game, Alli posted an image of him gesturing the scoreline to the home fans.
Tottenham manager Mauricio Pochettino, who has been linked with taking over at Manchester United on a permanent basis at the end of the season, called on Arsenal to find the culprit.
“Yes I saw. When we play a derby we hate each other in a good way, but that looks in a bad way when you want to damage some people,” he said.
“One stupid person made a mistake. I respect the Arsenal fans. I hope that Arsenal take some responsibility.
“Through the camera you can identify. It wasn’t a problem but it could be a big issue. I think they will identify the people.”
This comes after Tottenham fan Averof Panteli was fined and banned for four years for throwing a banana skin at Pierre Emerick-Aubameyang following his goal in Arsenal’s 4-2 win earlier this month.
Tottenham will play Chelsea in the Carabao Cup semi-final, with Manchester City hosting Sky Bet League One side Burton Albion in the other tie.
source: Sky News