Alli was a surprise absentee at Wembley after picking up a hamstring injury and he has also withdrawn from the England squad for upcoming friendlies against Germany and Brazil.
Harry Winks' place may also be in doubt after he twisted his ankle against Palace, coming off at half-time before Son Heung-min's strike sealed all three points for Tottenham.
Winks and Alli now face a fight to be involved against Arsenal at Emirates Stadium on November 18.
"Dele Alli against Manchester United finished the game feeling his posterior tendon, close to the hamstring, and then played 90 minutes against Real Madrid," Pochettino said.
"It's a very, very, very small thing. It was a massive risk (to play him) again. We're sure he'll be ready for Arsenal (after the international break). We hope he's going well in the next few weeks and will be available."
On Winks, Pochettino said: "He twisted his ankle. It's a little bit painful. We must assess him with our medical staff and with the national team medical staff too.
"He's so excited to play for the national team. I don't know [if he can play]. It's about him and both [teams of] medical staff."
The pair add to a lengthy list of Tottenham injury problems, with Hugo Lloris, Toby Alderweireld, Michel Vorm, Erik Lamela and Victor Wanyama all currently unavailable.
Harry Kane, who missed last weekend's defeat to Manchester United with a hamstring strain, also took a kick to his foot against Palace and the striker was substituted in the second half.
"We wanted after 75 minutes to protect Kane. He's okay, he's going with the national team," Pochettino said.
"The Christmas period is so tough for the players. You cannot do too much; only have good communication and a good relationship with the national team and explain the situation with everyone and trust they will manage them in a good way.
"We knew it would be a massive challenge for us to be ready again and fresh after [Wednesday's 3-1 defeat of Real Madrid]. But I am very pleased. The result was fantastic even if it wasn't our best performance."