Rooney was sent off in the second half for kicking out at Miodrag Dzudovic, with England leading 2-1 at the time.
It was thought that the Manchester United forward might be omitted from the side after the arrest of his father and uncle over match-fixing allegations just a few days prior.
However, the Italian opted to start Rooney and believes that he made the right decision in doing so.
"It was not a mistake," he said. "He was not happy because he missed some control and some passes. For this reason, I think he reacted. His reaction was to kick the opponent."
Rooney will now be suspended for England's first match at next summer's European Championships, and possibly more depending on a UEFA ruling.