Judge Thokosile Masipa said humans were fallible, and may not have heard gunshots or screaming as they thought.
Correspondents say this could make a premeditated murder verdict unlikely.
Oscar Pistorius, 27, denies murdering Reeva Steenkamp on Valentine’s Day of 2013, saying he thought there was an intruder.
The judge could also find him guilty of culpable homicide, or manslaughter, for which he would face a long jail term.
Oscar Pistorius has pleaded not guilty to all the charges he faces, including two counts of shooting a firearm in public and the illegal possession of ammunition.
Judge Thokosile Masipa began by detailing the charges against the athlete and repeating extracts of his testimony, reading in a slow, measured way.
She then moved on to a summary of the trial.
A tense-looking Oscar Pistorius looked on from the dock, and then began to weep.
Judge Thokosile Masipa said that defense claims that police contaminated evidence and removed items from the crime scene “paled into insignificance”.
She questioned the reliability of several witnesses who apparently heard screams and gunshots at the time of the incident, saying most of those who said they had heard the incident had “got facts wrong”.
The judge also said that the court would not make inferences about the state of the relationship between Oscar Pistorius and Reeva Steenkamp. The prosecution has suggested that it was “on the rocks”.
Correspondents say the judge appeared to be moving much more quickly than expected through the evidence, in a process which had been expected take hours or even days.
During his closing remarks last month, Oscar Pistorius’ lawyer Barry Roux conceded that the athlete should be found guilty of negligence for discharging a firearm in a restaurant – which carries a maximum penalty of five years.
Most of the trial, which began on March 3, 2014, has been televised and attracted worldwide attention.
Reeva Steenkamp, a 29-year-old model and law graduate, was hit three times by bullets shot through a toilet door by Oscar Pistorius at his home in the capital, Pretoria, in the early hours of February 14, 2013.
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