Rooney was handed the ban after being sent off for kicking Miodrag Dzudovic during the 2-2 draw with Montenegro in October.
The FA have put together a case – including a written letter by Dzudovic asking that the ban be reduced – that is to be put before the UEFA panel on Thursday.
"The sentence, three games, was too much for me and I hope the appeal will help us reduce the sentence," said Capello.
"I hope he'll be available for the third game. I hope they understand our lawyer, what Rooney says and what I will say at the committee."
Rooney will miss the three group games at the European Champions should the appeal be rejected.