They will be available to 66 developing countries in Africa, Asia, Latin America and the Caribbean.
Second-line treatment is required in patients who develop resistance to first-line drugs and currently costs ten times the amount of first-line therapy.
The new savings will result in a cut of 25 per cent in low-income countries and 50 per cent in middle income countries.
"Seven million people in the developing world are in need of treatment for HIV/Aids," said President Clinton.
"We are trying to meet that need with the best medicine available today, and at prices that low and middle income countries can afford. I applaud Cipla and Matrix for their commitment to lower the cost of new drugs at the forefront of the fight against Aids, and I thank Unitaid for the funds that have enabled us to make these drugs widely available."
A new once-a-day pill which is currently too expensive for the developing world to use will also become more readily available as a result of the new price deal.
The pill combines the drugs tenofovir, lamivudine and efavirenz and is associated with improved treatment outcomes. Its new cost represents a 45 per cent reduction from the current rate available to low-income countries and is a 67 per cent reduction from the price available to many middle income countries.
Commenting on the deal, French foreign minister Philippe Douste-Blazy, chairman of the Unitaid board, said: "Every person living with HIV deserves access to the most effective medicines, and Unitaid aims to ensure that these are affordable for all developing countries."
According to the joint United Nations programme on HIV/Aids (UNAids), there are about 40 million people living with HIV and three million people died of Aids in 2006.
Click here to run an energy price comparison, and see if you could be paying less for your gas and electricity.