Knox, 26, received word of the verdict in her hometown of Seattle. The former American exchange student called it unjust and said she was "frightened and saddened."
"This has gotten out of hand," Knox said in a statement. "Having been found innocent before, I expected better from the Italian justice system."
Lawyers for Knox and her ex-boyfriend Raffaele Sollecito, who was also found guilty, vowed to appeal to Italy's highest court, a process that will take at least another year and drag out a seesaw legal battle that has fascinated court-watchers on both sides of the Atlantic.
After nearly 12 hours of deliberations Thursday, the appeals court in Florence reinstated the guilty verdicts first handed down against Knox and Sollecito in 2009 for the slaying of British exchange student Meredith Kercher.
Those verdicts had been overturned in a second trial that ended in an acquittal in 2011, and Knox was released from prison after four years behind bars, returning to the United States. But Italy's highest court ordered a third trial.
The Florence court increased Knox's sentence from the original 26 years and handed Sollecito 25 years.
Kercher, 21, was found dead Nov. 2, 2007, in a pool of blood in the bedroom of the apartment she and Knox shared in the central Italian city of Perugia, where both were studying. Her throat had been slit and she was sexually assaulted.
Knox and Sollecito denied any involvement in the killing, insisting they were at Sollecito's apartment that night, smoking marijuana, watching a movie and making love.
Prosecutors originally argued that Kercher was killed in a drug-fueled sex game gone awry - an accusation that gave the case a lurid cast that fascinated the European tabloids.
But at the third trial, prosecutors argued instead that the violence stemmed from arguments between roommates Knox and Kercher about cleanliness and was triggered by a toilet left unflushed by the third defendant in the case, Rudy Guede.
Guede, who is from the Ivory Coast, was convicted in a separate trial and is serving a 16-year sentence for the murder.
Legal experts have said it is unlikely that Italy would request Knox's extradition before the verdict is final.
If the conviction is upheld, a lengthy extradition process will probably ensue, with the U.S. State Department ultimately deciding whether to turn Knox back over to Italian authorities to serve her sentence. Her lawyers are likely to argue that she is the victim of double jeopardy, because she was retried after an acquittal.
"Many Americans are quite astonished by the ups and downs in this case," said Mary Fan, a former federal prosecutor who teaches at the University of Washington Law School in Seattle.
But Fan said U.S. courts have previously held that being acquitted and then convicted of a crime in another country is not a legal bar to extradition.
U.S. Senator Maria Cantwell, a Democrat from Knox's home state of Washington, said she was "very concerned and disappointed" by the verdict and confident the appeal would re-examine the decision.
"It is very troubling that Amanda and her family have had to endure this process for so many years," she said in a statement. "I will continue to closely monitor this case as it moves forward through the Italian legal system."
Sollecito's lawyers said they were stunned by the conviction. "There isn't a shred of proof," attorney Luca Maori said.
Kercher's brother and sister were in the courtroom for the verdict and said the outcome was the best they could have hoped for.
"It's hard to feel anything at the moment because we know it will go to a further appeal," said her brother, Lyle Kercher. "No matter what the verdict was, it never was going to be a case of celebrating anything."
In his closing arguments, Knox's lawyer, Dalla Vedova, had told the court he was "serene" about the verdict because he believed the only conclusion from the files was "the innocence of Amanda Knox."
The first trial court found Knox and Sollecito guilty of murder and sexual assault based on evidence that include DNA and confused alibis. But the DNA evidence was later deemed unreliable by new experts.