The prosecution had asked for the evaluation after a psychiatrist told the court on Monday that Pistorius, who is on trial for the murder of Reeva Steenkamp on Feb. 14 last year, suffered from an anxiety disorder.
Prosecutor Gerrie Nel has argued he wanted to prevent the 27-year-old sprinter, who faces life in prison if convicted, from later appealing on the basis of a disturbed mental condition.
Defence lawyer Barry Roux had argued against the motion, saying it was premature to have the evaluation before he called other witnesses.
But Judge Thokozile Masipa ruled that a mental assessment would ensure that Pistorius gets a fair trial, adding that she thought it "strange" that the defence had opposed the motion.
Masipa said the court would hand down the details of the assessment on Tuesday. It would be preferable for Pistorius to undergo the evaluation as an outpatient, she said.
Pistorius, who has frequently vomited into a bucket and broken down sobbing during the trial, showed no emotion as he stood in the dock listening to Masipa's ruling.
"As a family we are comforted by the thoroughness and detail of this judgement," his uncle Arnold Pistorius told reporters outside the courthouse.
The evaluation is expected to take around 30 days and will prolong the trial which began on March 3.
The court will likely use the evaluation to determine whether Pistorius lacked "criminal capacity" at the time of the shooting due to his mental disorder, South African lawyer and legal expert John Welch said.
In that case, Pistorius could be sent to a mental institution for the rest of his life, Welch said. If Pistorius is judged to have a "diminished criminal capacity" the trial would continue, although the track star could receive a lesser sentence if convicted.
Pistorius has denied he killed Steenkamp in cold blood, saying he shot four times at the toilet door of his luxury Pretoria home to protect himself from what he thought was an intruder.
Pistorius competed against able-bodied sprinters on carbon-fibre prosthetics, becoming one of the most recognised names in athletics. He won a clutch of Paralympic medals and reached the semi-finals of the 400m at the London 2012 Olympics.
(Reporting by Siyabong Sishi, Nomatter Ndebele and Ndundu Sithole, Writing by David Dolan, Editing by Ed Stoddard and Angus MacSwan)
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