The 29-year-old hurt his knee playing for Western Province in Saturday's Currie Cup final victory over the Sharks, with scans revealing he will not be fit in time for the three-Test tour, which begins in Ireland on November 10.
Habana's is the latest in a series of injuries to hit Heyneke Meyer's squad, with the likes of Bismarck du Plessis, Pierre Spies, Frans Steyn, Schalk Burger and Juan Smith among those sidelined.
The list of absentees has, however, opened the door for five new faces - wingers Raymond Rhule and Lionel Mapoe, loose forward Arno Botha, lock Franco van der Merwe and scrum-half Jano Vermaak.
Full-back JP Pietersen and hooker Chiliboy Ralepelle have also returned to the squad following injury.
After the match with Ireland, the Springboks take on Scotland on November 17 before meeting England a week later.
Meyer said of the tour: "Although the Springboks won on their last visit to Dublin (in 2010), they lost three in a row before that.
"In 2010, we lost to Scotland in Edinburgh. They beat the Wallabies in Australia earlier in the year, so it won't be easy there.
"And in June we've experienced first-hand how difficult an opponent England are. They will be fired up at Twickenham and it will be a challenging Test to end the tour with.
"Our aim is to end the season on a positive note. The Rugby World Cup in 2015 also takes place in England, so we will use this tour to see how our players adapt to the conditions as we look ahead to that very important tournament."
The squad will gather in Cape Town in midweek before flying out on Saturday.
South Africa squad: Alberts, Botha, Brits, Cilliers, Coetzee, De Jongh, De Villiers (captain), Du Plessis, Etzebeth, Hougaard, Jantjies, Kirchner, Kruger, Lambie, Louw, Mapoe, Mtawarira, Mvovo, Pienaar, Pietersen, Ralepelle, Rhule, Steenkamp, Steyn, Strauss, Taute, Van der Linde, Flip van der Merwe, Franco van der Merwe, Vermaak, Vermeulen.