Habana returns after recovering from a knee injury which forced him out of the 49-3 win over Fiji on Saturday and takes the place of JP Pietersen, who drops out of the matchday squad.
Hougaard earns a start for the holders ahead of Fourie Du Preez after two impressive performances from the bench, including the match-winning try against Wales in the opening 17-16 win.
There was also a place in the side for winger Gio Aplon, flanker Willem Alberts and tighthead prop CJ Van der Linde as De Villiers resisted the opportunity to make wholesale changes to his team that are expected to easily overcome Namibia.
Flanker Heinrich Brussow dropped to the bench to make way for Alberts while winger Odwa Ndungane and prop Jannie Du Plessis were rested for the Pool D clash after starting against Fiji.
Hooker Chiliboy Ralepelle was the only switch on the bench for the Springboks as he took the place of Bismarck Du Plessis.
Locks Victor Matfield (hamstring) and Johann Muller (hamstring), centre Jean de Villiers (rib cartilage) and flyhalf Butch James (hip flexor) were not considered for selection because of injury.
South Africa are heavy favourites to win Pool D and after facing lowly Namibia at the North Harbour Stadium in Albany, they round off their group campaign against Samoa on September 30.
Team: 15-Pat Lambie, 14-Gio Aplon, 13-Jaque Fourie, 12-Frans Steyn, 11-Bryan Habana, 10-Morne Steyn, 9-Francois Hougaard; 8-Pierre Spies, 7-Schalk Burger, 6-Willem Alberts, 5-Danie Rossouw, 4-Bakkies Botha, 3-CJ Van der Linde, 2-John Smit (captain), 1-Gurthro Steenkamp.
Replacements - 16-Chiliboy Ralepelle, 17-Tendai Mtawarira, 18-Francois Louw, 19-Heinrich Brussow, 20-Fourie du Preez, 21-Ruan Pienaar, 22-Juan de Jongh.