Adam Jones dislocated his right shoulder after being charged by Bakkies Botha at a ruck in the second half.
He went to hospital where he had his shoulder put back into place under anesthetic. He will also be out for some time and will see a specialist on his return to find the full extent of the damage.
Centres Jamie Roberts and Brian O'Driscoll also went to hospital, along with Tommy Bowe, and face a race against time to recover for the third Test.
Roberts damaged his right wrist, although X-rays showed there is no fracture.
Lions doctor James Robson said: "It certainly was a fairly brutal game. As the casualty list goes it is not something I am happy with.
"To lose two of our most colourful characters in Gethin and Adam is distressing.
"We couldn't get Adam's shoulder to pop back in at the stadium and he was required to go to theatre. He will be subject to further investigation and specialist opinion."
Robson is optimistic about O'Driscoll's Test chances. The Ireland captain took two big hits on his head in clashes with Habana and Danie Rossouw but was alert and well on the morning after the game.
The severity of his concussion, and the time it takes him to recover, will now be subject to tests and examination by a neuro surgeon.
It is still possible he could be passed fit to play on Saturday, while his Irish team-mates Bowe and Ronan O'Gara are also hoping to be passed fit.
Bowe strained his left elbow, while O'Gara had stitches put into a deep cut on his left eye which bled into the eye.
Like Jenkins, he is staying behind in Pretoria to rest while the rest of the players take a two-day safari break to recharge their batteries ahead of the final game.