The pair will miss Tottenham's important game against Liverpool with thigh and hamstring injuries respectively.
Lloris, who pleaded guilty to a drink driving charge on Wednesday, sustained his injury in the 3-0 victory against Manchester United whilst Alli picked his up on International duty with England.
Lloris' is expected to be out for several weeks whilst Alli's injury is less severe and although unlikely he could yet return for Tottenham's Champions League match against Inter next week.
Mauricio Pochettino said in his press conference:
"Disappointed, because we're going to miss him for this game, and possibly Inter Milan in the Champions League, but it is not a big issue.
"Hugo Lloris will have another scan to see the evolution of his injury.
"Hopefully, it will be OK and he will be available again soon, like Dele."
It is expected that Mich Vorm will take Lloris' place against Liverpool, Alli could be replaced by Erik Lamela or Heung Min Son, who recently returned from injury and International duty respectively.