Habana, who scored two tries in the romp, will undergo a knee scan on Monday after taking a heavy knock during the tests.
While the Springbok management have not officially said how long the player will be out, it has been suggested that he could miss the home leg of the Tri Nations with a month out.
"We will have him examined properly on Monday and then give an indication of how serious the injury is," Bok coach Jake White said.
Habana scored two blistering tries to become the highest Springbok try scorer against England with five.
The 23-year-old surpassed the record held jointly by Danie Gerber and Joost van der Westhuizen, and took his try tally for the Boks to 21.