Blue Bulls fly half Francois Brummer extended his lead at the top of the leading points scorers table with a try of his own and three conversions to give the Baby Boks a 26-6 interval lead.
Second half tries from Halfpenny and Cardiff Blues prop Sam Hobbs made the scoreline respectable but Mapoe and Ebersohn both scored again and Frederick Kirsten put South Africa out of sight.
"It was a game too far for us," said Wales coach Patrick Horgan.
"We have taken some pretty tough knocks throughout the tournament and although the boys were desperate to finish on a high it was not to be. They are a fine side and they caught us out."