Knox and her Italian former boyfriend Raffaele Sollecito – originally sentenced to 26 and 25 years in prison for killing Meredith Kercher – were acquitted on appeal in 2011 after four years behind bars.
In an astonishing legal about-turn, the supreme court quashed the acquittal in March, and in the 74-page document summing up its decision, it cited "numerous examples of shortcomings, contradictions and incoherencies" in the ruling.
Among other things, it found fault with the time-scale of the murder that the appeals court had relied upon, saying that the "harrowing scream" heard by several witnesses pushed back the time of the crime.
Both Knox and Sollecito face a retrial in a Florence court, although no date has yet been set.
"We do not fear any further in-depth analysis because it will just make clearer the fact that Sollecito is extraneous to all the accusations," his lawyer Giulia Bongiorno told journalists.
Kercher, 21, was found half-naked with her throat slashed in a pool of blood in her bedroom in the house in the university town of Perugia that she shared with Knox in November 2007.
A third person, Ivory Coast-born drifter Rudy Guede, who like the other two accused has always denied the murder, is the only person still in prison for the crime.
Prosecutors alleged that Kercher was killed in a drug-fuelled sex attack, claiming Knox delivered the final blows while Sollecito and Guede held the victim down.
Investigators insist that 47 knife wounds on Kercher and the apparent use of two different knives in the attack meant that more than one killer had been involved.
Lawyers for Knox and Kercher's family refused to comment to AFP on the appeal court documents.