Botha has been ruled out of the remainder of the World Cup after suffering a recurrence of an Achilles injury in training.
Australia face the Springboks in Sunday's quarter-final at Wellington Regional Stadium and Alexander expects Danie Rossouw to prove a quality replacement for Botha.
"South Africa are a proud rugby nation, they keep producing one massive lock after another. They have a production line in the position," he said.
"Danie Rossouw is a great player. He's an excellent ball carrier.
"He's just as big and just as physical as Bakkies and has almost played as many Tests as Botha so they won't miss him that much.
"We know what a massive challenge it's going to be against South Africa, especially the physical side of it - the confrontations, the impacts, the tackle, the scrum, mauls and breakdown.
"We know where we have to be to get the result we want."
South Africa finished bottom of the Tri Nations but are third favourites to win the World Cup after topping a group that included Wales and Samoa.
"The Springboks are match-hardened now," said Alexander.
"They will be much better for the games they have played in the toughest pool and they will be match-fit.
"We have played some good rugby throughout the year and won the Tri Nations, but that counts for nothing as this is a new tournament.
"But we know from the work we have been doing on the training paddock and the work we have done before that we are capable of a good result and we draw on that for confidence.
"The Springboks fear no one, but I feel confident and ready to face them."
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