The win boosted South Africa to 1-1-1 in Group A play but, combined with Tuesday's other group result in which Uruguay defeated Mexico 1-0, wasn't enough to push South Africa into the knockout round.
Uruguay (2-0-1) finished first in Group A. Mexico was 1-1-1 but had a better goal differential than South Africa and so was advanced. France, a pre-tournament favorite that saw much controversy after early on-field disappointments, was sent home with a 0-2-1 mark.
Khumalo put South Africa ahead in the 20th minute. Siphiwe Tshabalala sent a corner kick across the box where Khumalo was able to head the shot past French goalkeeper Hugo Lloris.
France played much of the match down a man after Yoann Gourcuff was sent off in the 25th minute. About 12 minutes later, South Africa made the score 2-0 when Mphela converted a pass from Tsepo Masilela.
France got its first goal of the tournament 70 minutes into its final game. Florent Malouda had a clear shot after good work by Franck Ribery, before Malouda took the ball and drew the attention of South African goalkeeper Moneeb Josephs.
Aaron Carter is still in love with Hilary Duff
Ray Liotta sues skin care company over use of likeness