The Ospreys star has been recalled by caretaker coach Nigel Davies. Henson's last full Wales appearance was against Australia in November last year.
Davies has opted for an all-Ospreys midfield on Saturday, with Henson partnering Sonny Parker in the centre and James Hook featuring at fly-half.
It means that Cardiff Blues and World Cup centre Tom Shanklin moves to the wing, while Llanelli Scarlets' fly-half Stephen Jones has to content himself with a place on the bench.
Scarlets' full-back, 23-year-old Morgan Stoddart, will make his Wales debut - after injury ruled out Ospreys' Lee Byrne.
Cardiff Blues prop Gethin Jenkins will captain Wales, while his fellow prop - South Africa-born Rhys Thomas - is rewarded for some impressive form in Newport Gwent Dragons colours.
The back-row vacancy created by flanker Martyn Williams' post-World Cup retirement from international rugby is filled by his Cardiff colleague Robin Sowden-Taylor.
Davies said: "Gavin's partnership with both James Hook and Sonny Parker at the Ospreys has been going well of late, which is the main reason for going with that combination.
"We have had our hand forced a little in the backs with injuries to both Lee Byrne and Jamie Robinson ruling them out of contention, but the result is a pretty exciting new-look back line which I am sure can make South Africa stand up and take notice.
"Morgan has been in a rich vein of form of late, and if he can retain his composure in what will be a cauldron atmosphere at the Millennium Stadium and allow his talent to shine through, then he could make quite a debut."
Wales to play South Africa at the Millennium Stadium on Saturday: M Stoddart (Llanelli Scarlets); M Jones (Llanelli Scarlets), S Parker (Ospreys), G Henson (Ospreys), T Shanklin (Cardiff Blues); J Hook (Ospreys), D Peel (Llanelli Scarlets); G Jenkins (Cardiff Blues, captain), H Bennett (Ospreys), R Thomas (Newport Gwent Dragons), A-W Jones (Ospreys), I Evans (Ospreys), C Charvis (Newport Gwent Dragons), R Sowden-Taylor (Cardiff Blues), J Thomas (Ospreys).
Replacements: TR Thomas (Cardiff Blues), D Jones (Ospreys), L Charteris (Newport Gwent Dragons), A Popham (Llanelli Scarlets), M Phillips (Ospreys), S Jones (Llanelli Scarlets), T James (Cardiff Blues).