Hughes to captain Australia A
Henriques led the Australians during their loss to the South Africans over the past week, but he was unable to bat in the second innings due to the groin problem he picked up.
He will return to New South Wales for rehabilitation and will be replaced in the Australia A squad by Victoria seamer Clint McKay.
Queenslanders Michael Neser and Cameron Boyce have left the squad to take part in Queensland's pre-season camp, although their state team-mate Peter Forrest has remained with Australia A.
That means left-arm spinner Steve O'Keefe will likely play his first Australia A match of the winter and will be hoping to remind the selectors of the skills that made him the leading Sheffield Shield wicket taker last season, when he collected 41 victims at 20.43.
The second and final four-day match begins on Thursday.
Australia A squad Phillip Hughes (capt), Marcus Stoinis, Tom Cooper, Peter Forrest, Callum Ferguson, Matthew Wade, Peter Nevill (wk), Steve O'Keefe, Gurinders Sandhu, Chadd Sayers, Clint McKay, Jason Behrendorff.