Alli instantly clutched the back of his leg and then sat upright by the advertising boards, seemingly in considerable pain.
The incident ultimately resulted in the midfielder being replaced by Georges-Kevin Nkoudou with just four minutes of normal time left.
Speaking after the game manager Mauricio Pochettino was not sure how severe the problem is.
"It is in the left hamstring, I hope it is not a massive problem, but we will need to assess,” the Argentinian coach said.
“Some injuries appear in a period with a more busy schedule and another opportunity opens the door for players not consistently in the starting XI or on the bench. It is great opportunity for different players to show quality."
Should Alli be ruled out for a number of weeks it will come as real blow for Pochettino, who lost Harry Kane until March after the striker went down late against Manchester United.
Spurs also are without Heung-min Son, who is on international duty with South Korean, while Lucas Moura, Moussa Sissoko and Victor Wanyama are also injured for the foreseeable future.
However, Pochettino will be relieved by the return of Eric Dier. The 25-year-old midfielder missed the busy Christmas period after having his appendix removed but returned in latter stages on the win against Fulham.
That substitution proved vital for Tottenham, with Dier’s introduction meaning Harry Winks was pushed forward into a more offensive position.
It was from there that the Spurs No.8 made a match-winning contribution. Winks’ perfectly-timed dash into the box in injury time meant he connected perfectly with Nkoudou’s cross to score a dramatic late winner.
It had been Alli who had got the ball rolling early in the second period when his header brought Tottenham back on level terms.
Spurs face their London rivals in their next game on Thursday, in the Carabao Cup semi-final second leg, where all eyes will be on who Pochettino starts in the attacking areas of the pitch.