Knox is in the United States following a previous acquittal, but her former Italian lover Raffaele Sollecito was in court, awaiting what will be the fourth ruling in this high-profile case.
"The knowledge of Amanda's innocence is now rock-solid and it allows us to await the verdict with serenity," her lawyer, Carlo Dalla Vedova, told the court in his final arguments.
"It is not possible to convict someone because they are considered 'probably' guilty," he said.
Two judges and eight jurors retired to consider their verdict, which chief judge Alessandro Nencini said was not expected before 1600 GMT.
Knox and Sollecito spent four years in prison for the murder of Leeds University exchange student Meredith Kercher, who was found with multiple stab wounds and her throat slit in the house she shared with Knox in the town of Perugia in central Italy.
The two were acquitted in 2011 but the supreme court overturned that ruling in 2013, sending the case back for re-trial as Italy does not have laws against "double jeopardy" — prosecuting someone for a crime of which he or she had been acquitted.
The verdict expected later on Thursday might still not be the final word in the long-running case since both prosecution and the defence have the right to appeal again to the supreme court.
As he arrived for the hearing in a justice building on the edge of Florence, the 29-year-old Sollecito told reporters: "People who had it in for me thought I would not be coming".
Sollecito is not obliged to attend the trial under Italian law and his father, Francesco Sollecito, said that his son's choice showed "courage, respect for the court and faith in justice".
Sollecito has been travelling widely since he and Knox were acquitted and he had been living in the Dominican Republic in recent months, raising suspicion that he might be fleeing justice.
The 26-year-old Knox said she has not returned to Italy for fear of being "wrongly convicted". She and Sollecito both insist they are innocent.
If she is convicted, experts doubt that Knox could ever be extradited back to Italy, but the Seattle resident may not be able to travel freely outside the United States if Italy issues a warrant for her arrest. She has said she fears becoming "a fugitive".
A guilty verdict could see Sollecito back in jail or stripped of his passport to stop him fleeing Italy while the appeal process is exhausted.
Kercher's brother and sister were expected to be in court for the verdict.
"They are very tired of the ongoing judicial process and hope that they will get justice," the family's lawyer, Francesco Maresca, said.
The Florence court has focused largely on the presumed murder weapon – ordering fresh DNA tests on a kitchen knife found in Sollecito's apartment which have proved mostly inconclusive.
It is also being asked to consider Knox's initial admission that she was in the house at the time of the murder – which she later said had been made under pressure — and the fact that she falsely implicated a local bar owner, Patrick Lumumba.
Drug dealer Rudy Guede, whose DNA was found at the scene, is the only person serving time for the murder, but investigators say the knife wounds suggest there was more than one killer.
Dalla Vedova on Thursday said Guede had likely been caught by Kercher while he was burgling the house and had assaulted and killed her alone.
Prosecutors claim Knox's DNA on the presumed murder weapon – a kitchen knife found in Sollecito's house – and Sollecito's DNA on a bra clasp ripped off during the attack prove they stabbed Kercher while Guede raped her.