It was removed on Thursday following a shooting at his home in Pretoria.
The advert shows Pistorius dressed in a green lycra body suit coming off the starting blocks wearing his distinctive blades. The Nike "Swoosh" and its slogan "Just Do It" are shown on the advert.
Earlier, the international sportswear brand declined to comment on its future relationship with Pistorius.
"This is a police matter and is under investigation," Nike South Africa spokesperson Seruscka Naidoo said.
"From Nike we extend our condolences to everyone affected by this."
Nike is one of Pistorius's five major sponsors. He has appeared in a number of commercials for the company since 2008.
Nike's website was down on Thursday afternoon.
Pistorius's model girlfriend Reeva Steenkamp was shot dead in his home in Pretoria on Thursday morning.
Pistorius is in police custody and will appear in court on Friday.
Nooshin Erfani-Ghadimi, programme coordinator for the Wits Justice Project, said that the rights of prisoners to have their medical condition taken into account is enshrined in the Constitution.
Theoretically speaking this meant that prisoners with disabilities had to be treated as well as they would be outside prison.
But prisons were not ideal conditions. “Holding cells are normally not as crowded as the cells of people awaiting trial – which in some cases can be 200% full – but people can still be kept in terrible conditions,” she said.
Pistorious would probably be luckier than most prisoners because of his wealth and status. “He could have protection and a single cell, which Joe Bloggs would not have access to,” she said. If he did not get bail he would be moved to the Pretoria Central Prison’s remedial facility, she said.
There overcrowding is a huge problem, and prisoners only get one hour outside of their cell to exercise. Professor Bonita Meyersfeld, director of the Centre for Applied Legal Studies, said there were set international standards for how people with disabilities were treated in a country.
This included in people in prison. “Everyone living with a disability has to be facilitated by the state. And this duty becomes even more onerous when they are under the control of the state,” she said.
But South Africa was struggling with making its courts and prisons disabled-friendly. “It is an obligation that is probably not being upheld,” she said. – Additional reporting by Sapa