The striker was dropped from the Blues side that lost 4-0 to Watford on Saturday following his poor efforts in training recently.
Clark told reporters: "Nikola's response was fantastic, absolutely brilliant. I spoke with him on Monday morning and the two things I said were, I think he's an extremely talented footballer, and I've got a lot of respect for him as a guy.
"But he has to understand I've got my principles, my standards, my rules. As I said, there was no rant, no shouting, it was me just making a decision I felt was right."
Birmingham are currently 17th in the Championship, four points clear of the relegation zone.