Nair warned that it is too soon to judge the state's case, and he noted that a wide range of experts beyond Botha had worked on the initial phases of the investigation -- from ballistics experts to specialists in blood spatter.
"The pieces of the puzzle may not yet all be before me," he said.
Conditions of bail
Pistorius left jail in a Land Rover chased by paparazzi on motorcycles Friday afternoon after posting a cash bond of 100,000 Rand (about $11,200). Another 900,000 Rand (about $100,800) is due by March 1, Nair said. He headed to his uncle's home after his release.
He cannot return to the home where the shooting happened, has to give up his passport and can't go near an airport, Nair ruled. He also can't drink alcohol and must report to a police station every Monday and Friday.
The decision comes a day after the South African Police Service moved to remove Botha from the case.
Botha, a 22-year detective, is accused of seven counts of attempted murder after allegedly chasing and firing on a minibus full of people while drunk, according to officials.
A spokeswoman for South Africa's prosecution service said the accusations would be little more than a "speed bump" in the case.
Model Vanessa Haywood, a South African model who is friends with Pistorius, said the murder charge doesn't fit with the kind-spirited man she knows. And she said she can relate to Pistorius' story of being filled with terror at the thought of an intruder.
"It's not the safest place in the world," she said of crime-ridden South Africa, where murder and carjacking cases are common. "My own home is like a prison. His version of events isn't as far-fetched as people think it is."
Pistorius earned the nickname "Blade Runner" as he competed on special carbon fiber blades in place of more traditional prosthetic limbs. He was born missing bones in his lower legs, and doctors amputated his legs below the knees when he was 11 months old.
Pistorius attained fame as a symbol of triumph over adversity when won a challenge to compete in the London Olympics. While he failed to medal there, he smashed a record to win the men's 400-meter race in the Paralympic Games a few weeks later.
He is considered a national hero in South Africa.
Pistorius put his career on hold after his arrest, and sponsors Nike and Oakley suspended their contracts with him.
His coach said Friday before the bail decision that, should he be let out on bail, the runner would resume training.