With prop Coenie Oosthuizen also doubtful with a shoulder problem, the South African Rugby Union have announced that Gio Aplon and Dean Greyling had been added to the squad.
Kirchner was hurt late in the first half of the Springboks' 22-17 victory in the first Test in Durban on Saturday and did not return after the break.
He underwent a scan this morning and will be re-examined next week.
Oosthuizen, who made his debut off the bench at Kings Park, has been suffering stiffness and will have a scan over the next day.
Coach Heyneke Meyer said: "We are not going to risk any player that is struggling with injuries and it was decided to call in replacements for both Zane and Coenie.
"Both Dean and Gio were on our official list of standby players and we're fortunate that both of them have played Test rugby for South Africa before.
"They have also been in good form in Vodacom Super Rugby and were two of the unlucky players that did not make the initial 32-man squad."
Aplon, 29, won the last of his 16 caps against Namibia in last year's World Cup while Greyling, 26, has played twice for the Springboks.
Kirchner and Oosthuizen will both remain with the squad for the time being.
The Springboks host England in the second Test at Johannesburg's Coca-Cola Park on Saturday.
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