Barton was dismissed by referee Mike Dean after an apparent elbow on Carlos Tevez and kicked out at Sergio Aguero before attempting to headbutt City captain Vincent Kompany as he was dragged from the pitch.
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The FA has since charged Barton with two acts of alleged violent conduct, but Fernandes will ensure that the matter is dealt with internally.
"I know Mark and Phil are talking about those kinds of things. It is too premature at the moment," he told Sky Sports News.
"We will have to wait and see and evaluate everything, and look at everything in retrospect. But that I'll leave to the manager and the CEO. I will not step in."
QPR maintained their Premier League status despite the loss at the Etihad Stadium thanks to Bolton's failure to win at Stoke, and the events have left the 48-year-old, who took over in August, looking to the future.
"For the moment we just want to focus on the positives and it is a little bit early to talk about that," he added.
"I'm still kind of walking on air to be honest, I have a smile from here to Malaysia.
"The chance to go and build something at QPR was too enticing an opportunity to miss, but the drama of yesterday and the feeling of today has made it even better." he continued.