Ireland coach Joe Schmidt now faces a difficult decision on who will replace him, but he is unlikely to call up injury cover to join the squad ahead of the final match in Port Elizabeth.
The visitors had led 19-3 at half-time but South Africa fought back with four tries in the second-half to tie the series at 1-1.
The damage had already been done when Henshaw was taken off and Schmidt now has a tough call on his replacement with Ulster duo Luke Marshall and Jared Payne likely replacements.
Marshall started in the first Test win and though Payne has turned out at full-back in his last two Ireland outings, he has won the majority of his 16 caps in the centre.
And with Connacht's Tiernan O'Halloran another contender for the No.15 shirt, Schmidt carefully considering his options.
"There are options with Marshall still being in the squad. That was Luke's first full Test for us last week for a long time and I thought he did a super job," said Schmidt.
"He's played a fair bit at 13 this year so he would be one option, as would Payne. He could slip back up into the 13 spot and Tiernan O'Halloran could go into the number 15 spot."
However, the Ireland coach has admitted they are unlikely to call up another player to the squad, with their current options deemed enough for the final Test despite the injury.
"To be honest, if we can cover it internally we probably will at this stage," said Schmidt.
"It's pretty difficult to get them up to speed and to get them down here is a bit of a mission even."
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