Despite missing most of the 2006–07 season due to a shoulder injury, Nesta played a vital part in Milan's return to the 2007 Champions League final, where Milan avenged their 2005 final loss, defeating Liverpool 2–1 in Athens. Despite Milan's point deduction during the season, Nesta was also able to return from injury in time to help Milan manage a fourth-place finish in Serie A, clinching the final Champions League spot. Nesta was elected to be part of both the UEFA Team of the Year and the FIFPro World XI for his performances that season.