The 32-year-old bowler is the first black African to reach 100 caps but has been criticised for some recent form, with suggestions he is past his best.
“He’ll stay as long as he does a job, if not, another player will be picked,” Gerald Majola told BBC Sport.
“There’s no issue he’ll play because he’s a black African, that’s definitely not our mandate to the selectors.”
Ntini’s appearance in the first Test of the current series against England was the 100th of his career, making him only the fifth player to reach 100 caps for South Africa.
But the 32-year-old took just two wickets in the drawn first Test in Centurion, while debutant Friedel de Wet – in for the injured Dale Steyn – almost bowled South Africa to victory with a hostile spell of 4-55 in the second innings.
But De Wet was omitted from the Proteas side for the second Test in favour of the fit-again Steyn, while Ntini was guaranteed his place before the match by captain Graeme Smith.
Majola said Ntini’s contribution to South African cricket went far beyond his efforts on the pitch.
“We can’t thank him enough,” he added.
“He’s the true ambassador – he has done more than any of one of us because he’s visible, he’s out there in the middle.
“He has inspired a lot of people to come and play the sport, and made sure the game is played by everyone – we can’t thank him enough.”
And Majola insisted Ntini was not receiving preferential treatment on racial grounds.
“He’s been dropped in the one-day side – if he performs he’ll play, if he doesn’t we’ll find someone else.”
Racial quotas have played a significant role in South African cricket since they rejoined the international arena, with a prime example being Kevin Pietersen’s decision to pledge his allegiance to England because he felt positive discrimination reduced his chances in South Africa.
Of the current England side, Pietersen, Jonathan Trott, Matt Prior and captain Andrew Strauss all have South African connections, but Majola said they were not worried about losing out on players.
“Anybody’s free to play wherever they want – we have enough talent in this country,” he said.
“We’ve just seen a few people coming through – Alviro Pietersen scored a few 50s in the one dayers, no one knew about him before.
“We’ve got plenty of players coming through the system. Whoever feels like going and getting a better chance somewhere else, we welcome it.”