Michael Hausfeld, one of the lawyers representing the South African plaintiffs, said the verdict was "a major advancement in international law".
The lawsuits argue that the car-makers knew their vehicles were being used by South African forces to violently suppress protests.
"That level of wilful blindness in the face of crimes in violation of the law of nations cannot defeat an otherwise clear showing of knowledge that the assistance IBM provided would directly and substantially support apartheid"
They also claim that IBM and Fujitsu knew their computers were being used by South Africa's white minority government to help strip black citizens of their rights.
Apartheid ended in 1994 when South Africa held its first free elections, bringing Nelson Mandela and the African National Congress to power.
The judge disagreed with arguments made by the companies that it was not their responsibility to tell clients how to use their products.
"That level of wilful blindness in the face of crimes in violation of the law of nations cannot defeat an otherwise clear showing of knowledge that the assistance IBM provided would directly and substantially support apartheid," she said.
Scheindlen allowed lawsuits against IBM for "aiding and abetting arbitrary denationalisation and apartheid".
She said that the plaintiffs could pursue claims against Daimler, GM and Ford "for aiding and abetting torture... extrajudicial killing, and apartheid".
And against Rheinmetall, the German parent company of Swiss-based arms manufacturer Oerlikon, for "aiding and abetting extrajudicial killing and apartheid".
Khulumani, a South African organisation that helps apartheid victims and is one of the plaintiffs in the court action, hailed the court decision.
"We are convinced that this lawsuit, should it be successful, will go a long way in satisfying members' material needs; and that will go a long way in contributing to social reconciliation," said Marjorie Jobson, a Khulumani director.