Du Plessis had to watch from the dressing room as his side went down to MI Cape Town by 36 runs at the Wanderers, and could not come out to bat in a massive 234 run chase.
Flemming confirmed after the match that du Plessis’ thumb was so bad that he could not even hold a bat, and he’s started preparing for the worst.
"Today he got his thump jammed in the ground which has done some damage. Obviously enough damage not to bat which was [not good], when you are chasing 200 you need your star players to be out there,” Flemming.
“So, to lose him is another factor but we'll take into consideration what happens going forward, we are hoping it's bruising and settles down but I feel overly optimistic with the amount of injuries we've had so far.
“A bit of a pessimistic view on these things, so I'm hoping for the best but we may have to prepare for other means."
Flemming believes that they have been a bit unlucky in the last three games.
They lost to the same team in Cape Town after the game was reduced to 12 overs, then had to share points after rain again had the final say on Thursday against Paarl Royals.
He’s confident that their players are mentally fit enough to not let the slump affect them.
"We began in Cape Town with a game on the wrong side of the weather, a short chase game so we carry a little perspective with the win or lose. We don't get carried away with those ones, we've had a good game here, we thought we had a good score in our last game and we didn't have a chance to defend,” the coach added.
“Today we thoroughly outplayed but given that we had our star batsman down and we still got a 200 and for us to come out of the blue and play innings. There are still some things and Vince is in good form.
“We did well to actually keep some resilience and deny him a bonus point and get close to 200. If you are getting 200 every game, you are not gonna be too far away."