Nduli was stretchered off in the first half following a heavy challenge from AmaZulu striker Thando Ngwenya, leaving Ouaddou concerned about the midfielder’s condition.
Referee Luxolo Badi opted to show Ngwenya a yellow card for the challenge, despite being close to the incident.
For Ouaddou, the biggest concern was seeing Nduli suffer another setback after recently returning from a lengthy injury layoff.
"We had to take him off because, unfortunately, he could not continue," Ouaddou said after the match.
"One of the top players that I admire so much. When you see a player and just go back from a long-layoff injury and again, he comes off the field, you get worried."
The Pirates coach believes South African football needs its best players available and wants them protected regardless of which club they represent.
"We want to see all our top players in the country, whether they are playing for AmaZulu or Pirates, or any other team, it doesn’t matter," he added.
"All the top players have to be seen on the field and showcase their talent. So, I wish him a speedy recovery."
Nduli’s injury overshadowed an otherwise frustrating evening for Pirates, who were held to a draw despite taking the lead.
AmaZulu responded through Ngwenya, who converted a first-half stoppage-time penalty to secure a point for Usuthu.
The result, however, extended Pirates' unbeaten run against AmaZulu in Durban to 18 matches.
Ouaddou will now hope Nduli's latest injury is not serious and that the midfielder can return to action without another lengthy spell on the sidelines.