Botha, 32, will miss Sunday's World Cup quarter-final clash against Australia because of an Achilles tendon injury and is unlikely to recover before the tournament ends.
The Blue Bulls lock is then set to join wealthy French club Toulon, where his team-mates will include England fly-half Jonny Wilkinson.
"Bakkies had a talk to the team this morning and it did get a little bit emotional," Habana said.
"We've had a guy that has really given his heart to this country for the last 10 years and he has become a good friend to a lot of us.
"He is a strong character within this team, not only by the way he carries on off the field, but his ability to bring this team together on the field.
"Yes, it was a bit sombre in the team room, and I think Bakkies said it the most - he said you never know when it's going to be your last game.
"I think it is tough on the team.
"Whether it was tougher losing Frans Steyn, or New Zealand losing Dan Carter, it's difficult to say, but he has become a great friend, a great rugby player and the ability he had to lift this team will live in our hearts for quite a while."
Danie Rossouw and Victor Matfield will forge South Africa's second-row pairing this weekend, while Jean de Villiers replaces an injured Steyn and prop Gurthro Steenkamp is preferred to Tendai Mtawarira.
The Springboks side is the most experienced in their Test match history, containing a total of 836 caps to surpass a previous record of 815 set against opening Pool D opponents Wales in Wellington last month.
The team includes eight players who started the 2007 World Cup final against England in Paris, plus three players who were part of that squad.
South Africa are bidding to become the first team to successfully defend the World Cup, with victory on Sunday meaning they will play New Zealand or Argentina in the semi-finals.
"We are expecting a great confrontation on Sunday," Habana added.
"They (Australia) have got the edge over us at the moment, but in a knockout game that means nothing. It's a do-or-die game for 80 minutes. I don't think history will count too much.
"On the day it's going to be about the accuracy of the execution and making sure that in a Test match where there might not be a lot of opportunities, that you use those opportunities to the best of your ability.
"In a competition like this, it is going to come down to decision-making. The team and individuals that make the best decisions and the most accurate decisions will come out on top."
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