"He's got to do some work today and possibly tomorrow as well to make sure that he's 100 percent," Du Plessis told a pre-match news conference.
"It's a tricky one, because we're in a position now where we need to win five games out of five. So you want to have your best guys available for selection."
But Du Plessis said he and coach Ottis Gibson had still to decide as South Africa sit with one point from the first four games.
"Probably the right call to make would be to say that if he's not ready, you just give him a little bit more time to see if he can play the next four games, which is going to be big."
After Afghanistan, South Africa play New Zealand, Pakistan, Sri Lanka and Australia before the group stage ends on July 6.
Ngidi's injury came on top of the withdrawal from the tournament of fellow speedster Dale Steyn, in two major blows to South Africa's hopes.
"We have to make sure that we try and put all of our energy and focus into the now and what's coming up next. I truly believe if we stay, if we carry those ghosts of the last week with us, then it's going to be tough to get out of the hole,” Du Plessis said.
"If you're looking back, then we're just going to almost like float through this tournament, win maybe one, maybe two, three games, but we're not going to achieve what we want.
"The fact there's been a bit of rain has given me clarity on the discussions we need to have on the team, and I feel that's been really good off the field," he said.
(Reporting by Mark Gleeson in Johannesburg; Editing by Hugh Lawson)
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