Rooney scored an 87th-minute penalty to earn United the win and book them a place in the last 16 of the Champions League.
The England international made his first start since the recent contract trouble.
“It took a lot of courage to take the penalty kick,” Ferguson said on ITV.
“It was not an easy night, he missed a couple of chances but that’s what you expect with the rustiness in his game. We are pleased for him.”
He added: “Every time he scores a goal he wants to celebrate with the fans and players.”
Ferguson has admitted that United are looking to top the group.
“We want to go and win the group,” added Ferguson. “We’ve got Valencia at home, we can look forward to that.”
