The England international made his way off the pitch late in the contest, and according to Telegraph Football he seemed to be holding his hamstring:
After the match, manager Mauricio Pochettino told reporters Alli had to be assessed, but noted the injury "doesn't look great."
Alli had scored the equalising goal in Tottenham's 2-1 victory at Craven Cottage, heading in Christian Eriksen's cross to cancel out Fernando Llorente's early own-goal. Harry Winks secured a dramatic 2-1 victory for the visitors when he headed in the winner deep into injury time.
At the age of 22, Alli is already one of Spurs' biggest stars and a key fixture in the England national team.
He often tucks in behind Harry Kane in an attacking-midfield role, using his chemistry to link up well with the striker in the final third and pushing up to provide Spurs with another option in and around the penalty area.
Alli can also play in a more traditional central-midfield role, although he's not quite as effective when it comes to the defensive side of the game.
With the likes of Eriksen, Winks and Eric Dier in the squad, Spurs still have a number of ways of lining up. Without Alli, though, they are lacking a major contributor of goals.
Compounding the problem is the absence of Kane due to injury, while Son Heung-min is also not available for selection due to his participation in the Asia Cup.
Spurs will face Chelsea in the EFL Cup in their next outing on Thursday.