The two companies will promote over-the-counter products, along with prescription drugs in areas including asthma, dermatology, high cholesterol, high blood pressure, migraine, and osteoporosis, Merck said.
It did not disclose financial terms of the deal.
Merck is second behind Pfizer Inc. among the world's biggest drugmakers by revenue. Its top sellers include the asthma drug Singulair, and Vytorin and Zetia for high cholesterol.
The drugs will be jointly marketed by Merck's MSD South Africa and by Adcock Ingram.
Merck, based in Whitehouse Station, N.J., said it expects emerging markets like South Africa to provide more than a quarter of its pharmaceutical and vaccine revenue by 2013.