South Africa 46 - 9 Samoa
I'd be very surprised if South Africa scored 46 points versus Samoa. Samoa's defense has been pretty strong during this tournament: they have only conceded 36 points in all their games so far. Both South Africa and Samoa easily beat Fiji and Namibia (though South Africa's wins were more convincing), and both had very close matches versus Wales. I think South Africa will certainly start as strong favourites, but people who think it will be an easy win for South Africa may be in for a big shock! Samoa is reasonably strong up front, though will need to be at their best to match South Africa in the tight exchanges. I think South Africa do have a clear edge at the lineout; Samoa's lineout has been ok, but they have been losing 2-3 throws per game, so I imagine Matfield could cause some problems. South Africa again have an edge in the loose; I expect Brussow will cause a lot of problems for Samoa. South Africa have some strong ball runners in the pack (du Plessis, Mtawarira, Rossouw, Spies, Burger), but I actually think Samoa match them here, with Johnson, Sshwalgher, Tekori, Stowers, Fa'asavalu, and Tuifua all noted ball runners.
Where I think Samoa may attempt to exploit South Africa is close to the fringes of the ruck (either with Fotuali'i himself, or with forwards running off his shoulder), as the lateral defense of some of the South African is not that good (though the fact that John Smith isn't there means there will be far fewer gaps to exploit!). I expect Samoa will send quite a few ball runners down Morne Steyn's channel too, so I expect Brussow and Burger will be doing a lot of tackling! I like the inclusion of Fuimaono-Sapolu in the midfield as he should add some creativity to Samoa's attack, but I do worry about how he will go defending F Steyn and Fourie. There are some great matchups out wide -if Samoa can make some space for their outside backs they could cause a lot of problems (Paul Williams in particular has looked in outstanding form).
Overall I still think South Africa will win due to there slight advantage in the tight, and their obvious advantage at the breakdown, but I suspect it will be pretty close. I'm picking South Africa by 10.