He is one of only three players retained from the side which defeated Sharks 71-31 at Loftus Versfeld on Saturday evening. The others are Anthony Watson, who moves from wing to full-back, and stand-off Dan Biggar.
Harris also changes position, reverting to his more usual outside centre role after being picked at inside centre against the Sharks, against whom he scored a try.
The only other Scot in the squad is tighthead prop Zander Fagerson who is named among the replacements.
The Lions have now decamped to Cape Town where they are likely to be based for the remainder of the tour.
Warren Gatland, the head coach, said last week that he anticipates all three Test matches being played there.
“We’re pleased to have arrived in Cape Town as we near the halfway stage of the Series,” said Gatland.
“Wednesday’s game against South Africa ‘A’ will be our toughest encounter since we arrived here and we’re looking forward to it. We expect them to be physical in the contact area and look to test us at scrum time.”
“I think we’ve benefitted from playing at altitude in the first three games. While the boys have felt it in their lungs, they’ll be all the better for it now we’re at sea level.
“As we move towards the business end of the Tour, it’s pleasing to see so many players putting in some stand-out performances. As coaches we want the players to make Test selection as hard as possible and that’s we’re seeing.”
British & Irish Lions team (v South Africa A, Wednesday, Cape Town Stadium, 7pm BST)
15. Anthony Watson (Bath Rugby, England)
14. Louis Rees-Zammit (Gloucester Rugby, Wales)
13. Chris Harris (Gloucester Rugby, Scotland)
12. Bundee Aki (Connacht Rugby, Ireland)
11. Josh Adams (Cardiff Rugby, Wales)
10. Dan Biggar (Northampton Saints, Wales)
9. Conor Murray, captain (Munster Rugby, Ireland)
1. Wyn Jones (Scarlets, Wales)
2. Ken Owens (Scarlets, Wales)
3. Kyle Sinckler (Bristol Bears, England)
4. Maro Itoje (Saracens, England)
5. Iain Henderson (Ulster Rugby, Ireland)
6. Josh Navidi (Cardiff Rugby, Wales)
7. Tom Curry (Sale Sharks, England)
8. Taulupe Faletau (Bath Rugby, Wales)
16. Luke Cowan-Dickie (Exeter Chiefs, England)
17. Mako Vunipola (Saracens, England)
18. Zander Fagerson (Glasgow Warriors, Scotland)
19. Adam Beard (Ospreys, Wales)
20. Tadhg Beirne (Munster Rugby, Ireland)
21. Sam Simmonds (Exeter Chiefs, England)
22. Gareth Davies (Scarlets, Wales)
23. Elliot Daly (Saracens, England)