Spurs picked up all three points at Fulham as Harry Winks struck at the death to earn a 2-1 win, but the victory came at a cost as Alli limped out of the action.
Another injury to an attacking player is the last thing Pochettino needs, given the absence of the injured Harry Kane and Son Heung-min, who is on international duty, over the next few weeks.
It looks highly unlikely that England international Alli, who has already been out twice this season with hamstring problems, will be fit to face Chelsea in the Carabao Cup semi-final second leg at Stamford Bridge on Thursday.
"You know very well the action," Pochettino said.
"We need to assess him in the next few days. The hamstring is a muscle we need to be careful with, but it doesn't look great. On the pitch, we all agree that when you see him put his hands on his hamstring you feel it's not great."
Alli's likely absence is at least off-set by the potential return of Lucas Moura, who has been working at the club's training ground following a knee injury.
"We're going to go there expecting to win. Like I told you with Kane, and now with Alli, we hope it's not a big issue," Pochettino added. "We hope Lucas Moura, who was training today at the training ground, is going to be OK.
"Today we didn't want to take a risk with him, but he's nearly 100 percent. Maybe it's not going to be Dele Alli, but we can have Lucas Moura on the bench or starting at Chelsea."