Alli headed Spurs level at Craven Cottage on Sunday, cancelling out an own goal scored by striker Fernando Llorente, but he could not complete the match.
The England international injured his hamstring and had to be replaced by Georges-Kevin Nkoudou, who created the 93rd-minute winner for Harry Winks.
With Harry Kane already sidelined until March, Spurs can ill afford Alli to be ruled out for any stretch of time, admitted concern after the match, confirming the injury to the left hamstring and saying the club would assess the problem in the coming days.
However, speaking later at a post-match news conference, Pochettino sounded more pessimistic over the situation, saying: "We need to assess him in the next few days but the hamstring is a muscle that you need to be careful with, the mechanism of the injury.
"We need to assess in the next few days, but of course it doesn't look great.
"On the pitch, I think we all agree that when you see him put his hand on his hamstring it's a situation where you feel...it's not great to see that."
Despite Alli's injury, Pochettino was thrilled with the character shown by his side as they bounced back from a 1-0 Wembley loss to Manchester United last time out.
"I am so excited now, the end was amazing and showed you always need to believe in your team," he said to Sky Sports.
"It was a solid performance, maybe not great. Fulham are a team that needed to win and show their quality and of course we struggled a little bit from set pieces.
"I am happy, because after Manchester United it was a very tough week for us, around the team some negatives but we have turned them into positives today. Today for different players there were massive opportunities to step up.
"I think it was fantastic for Nkoudou, I think his first league game it was important. In the 93rd minute for us to build from the back and for Winks to arrive in the box. That is the belief that we love to see from the players."
Even Llorente, deputising for the injured Kane and wasting a string of fantastic chances on top of the own goal he scored, earned Pochettino praise.
"He was good, I am so happy with his performance," Pochettino said of the striker, who was making his first Premier League start of the season.
"I think his performance was very good, he helped the team in the 93 minutes. Of course he has a few clear actions to score. That is the most important.
"It was tough for him to compete but he deserves now the opportunity. He's very professional and a very good player."