The new deal will keep the 29-year-old at Pride Park until the summer of 2015.
"Shaun remains very much part of our plans and it's important for him to know that, and we're very pleased he has extended his contract," Derby boss Nigel Clough told the club's official website.
"We've strengthened the defence in Shaun's absence with the arrival of Richard Keogh, and the availability Jake Buxton, while Mark O'Brien, Valentin Gjokaj, Tom Naylor and James O'Connor provide us with quality and experience.
"Shaun is a true leader and while we're missing his qualities on the pitch, we're not missing out off the field. He is playing a pivotal role in the changing room with the lads, which we knew he would do.
"He has a huge part to play this season despite not being available for selection and he's making steady progress. As we said when the injury was announced, we're going to be with him every step of the way."