The Cameroon international suffered suspected ligament damage to his left knee after a tangle with Lumana Lualua in the second half of the 1-0 reverse.
However, he travelled back with the team from Fratton Park and will be assessed further at Spurs Lodge in the morning.
Head Coach Jacques Santini said afterwards: "It was not a good night because we lost the game and lost Thimothee Atouba with a bad injury on his knee.
"I'm not sure at the moment but I think it could be quite a bad injury."
Thimothee Atouba was stretchered off with a knee injury in Monday night's defeat at Portsmouth.