Ferguson was part of Australia's 2009 ICC Champions Trophy-winning squad in South Africa, which he described as the "hugest" event of his career so far. During the tournament's final against New Zealand, Ferguson injured his knee while fielding. He would have been prepared to bat in Australia's run chase if needed, though later tests revealed that he would require a knee reconstruction, taking out of competitive cricket for at least six months. Despite not being able to play for the rest of the season, Ferguson kept his contract with Australia. Ferguson came back from injury to be named in Australia's squad for their ODI series in India in October 2010, but persistent rain meant he was unable to play any matches and he was then left out of Australia's squad for the next ODI series against Sri Lanka until a back injury forced Shaun Marsh out of the team.