Malan was injured in the match when he slipped on the wet turf as he tried to tackle New Zealand fullback Beauden Barrett. Television directors did not show replays of the incident.
After a lengthy stoppage, Malan was taken from the field on a stretcher after 18 minutes to applause from around the ground.
"From a physical point of view, he was operated on last night. There's a fracture and a dislocation, so it’s quite tough for him," coach Allister Coetzee told reporters Saturday.
"The sooner they did the operation, the better for his recovery and also for the season ahead. It was a very successful operation."
Coetzee said the New Zealand team had gifted Malan a signed jersey from their entire squad.
"That is not just saying the ethos and the culture and the values of rugby, but actually living and feeling it. That to me is unbelievable of the All Blacks to do something like that," he said.
The coach confirmed they will name a replacement in the coming days.
"We will make the call shortly. It will be an outside back. We’ve got a couple of names that’s up for discussion now in our coaches meeting," he said.
Malan was born in Windhoek but schooled at Paarl Boys High outside Cape Town, which is noted for producing South African internationals.
He had a spell in the academy of the Durban-based Sharks, where he also broke his ankle but now plays for the New England Free Jacks in Major League Rugby in the United States.
"The Free Jacks family stands by Le Roux as he navigates the recovery progress," his club said in a statement.
Malan was not the only casualty on the night, as Namibia loose forward Adriaan Booysen suffered a dislocated shoulder.
"It came back (into the joint) easily but we don’t know the extent of the trauma in the shoulder at this point in time. We’ll make a final call on him, I don’t want to rush that call."
