The Terriers will become the second team to lodge a formal complaint over the state of the Don Valley turf after Rochdale voiced their concerns last month.
The Don Valley Stadium played host to rock group U2 on August 20, leaving half of the pitch discoloured and worn.
Clark feared for his players safety and told BBC Radio Leeds: "Professional football shouldn't be played on that pitch. It was worse than a park pitch and I'm glad we've won the game because I can say that now."
He added: "I went in to see the referee an hour before the kick-off to tell him my concerns and we will be putting our disappointment down in written form.
"That's not having a go at the people at Rotherham United - it's the situation with the stadium."