Toyota said the 27-year-old German is also doubtful for the season-ending Abu Dhabi Grand Prix on November 1.
Glock crashed heavily and gashed his leg in qualifying for the Japanese Grand Prix at Suzuka on October 3 after missing Friday practice due to a fever and heavy cold.
Toyota said subsequent medical checks in Germany showed he had cracked a vertebra when he slammed head-on into a tyre wall.
"Obviously everyone in the team is very disappointed and feels for Timo; we wish him a very speedy recovery," said Toyota motorsport president John Howett in a statement.
"Based on the initial diagnosis, we fully expected Timo to return in Brazil but unfortunately a different injury has been revealed which prevents that.
"He will remain in Germany to recover and we hope he can recuperate in time for Abu Dhabi, although at this stage the situation is not clear," added Howett.
Reserve driver Kobayashi, 23, stood in for Glock in a rain-hit Friday practice at Suzuka.
"Kamui was the natural choice to step in and he proved in Suzuka that he is capable of holding his own," said Howett.
"It is a difficult task for him but he knows the team will give him its complete support and we know he is motivated to make the most of this unexpected opportunity."
Kobayashi's surprise call-up will double the number of Japanese drivers on the Interlagos starting grid next Sunday with Williams's Kazuki Nakajima currently the country's sole representative.
Nakajima has yet to score a point this season in 15 starts.
Glock finished second in his last race, the Singapore Grand Prix on September 27 but his future at Toyota had been uncertain before his accident with Howett suggesting that the team could opt for an all-new lineup in 2010.
Toyota have already allowed their option on Glock to lapse, with Howett saying in Suzuka Glock could still be in the car next year but the team wants to keep all their options open.
Mosley calls F1 deal into question
F1 teams appoint Montezemolo as chairman
Bernie talks of breakaway F1
Alonso move jumpstarts F1 merry-go-round
Vettel on pole after crash-hit qualifying