"It sends a clear signal to the African heads of state that lives should and can take precedence over patents," the statement adds.
Outside the court, demonstrators and activists, many of them Aids sufferers, danced and cheered when they heard the news.
The drugs companies had taken the government to court in an attempt to block legislation which gives it powers to import or manufacture cheap versions of brand-name drugs.
Now, the South African authorities are expected to enact the law, which they have argued is desperately needed to tackle the country's Aids crisis.
International welcome
The World Health Organisation and the International Aids Society, which represents specialist Aids doctors and researchers, welcomed the development.
"The outcome of the case signals a dramatic shift in the balance of power between developing states and drug companies," Oxfam, Medecins Sans Frontieres and the South African Treatment Action Campaign said in a joint statement.
"It sends a clear signal to the African heads of state that lives should and can take precedence over patents," the statement adds.
A spokesman for GlaxoSmithKline, one of the companies involved in the legal action, said an "amicable settlement" had been reached with the South African Government, and that Pretoria had made a commitment to respect international laws on drugs patents.
The BBC's Jane Standley in Pretoria says the pressure will now be on the government to come up with a treatment plan for the 4.7 million people estimated to be HIV positive in the country.
Public relations trouble
President Thabo Mbeki's administration has not yet said whether it will import retroviral drugs, which help prevent HIV turning into full-blown Aids, or if it will buy medication to treat so-called "opportunistic infections" that affect Aids patients.
Wednesday's hearing was adjourned, as the companies carried out intense negotiations aimed at securing a quiet exit from a case that correspondents say left them with a public relations disaster.
They have been accused of putting profit before the lives of millions of people who are unable to afford life-saving drugs in the developing world, a charge which they deny.
Blueprint
Mirryena Deeb, chief executive of the Pharmaceutical Manufacturers' Association of South Africa (PMA), said the government had agreed to consult the companies when the regulations to implement the law were drafted.
The new settlement could become a blueprint for future relations between pharmaceutical companies and governments in the developing world.
Legislation passed in 1997, which allowed for cheaper drugs, was suspended pending the outcome of this court case.
The South African Government argued that this tied its hands at a time when it desperately needed cheap drugs to address the country's crippling Aids crisis.