Homosexuality remains taboo in many socially conservative African societies.
Vivian Boyack and Nonie Dubes exchanged vows at the First Christian Church in Davenport on Saturday.
Transgender rights activists said the verdict was a great step towards ending discrimination.
Zuma says SA respects Uganda’s right to adopt its own law, even if it criminalises homosexuality.
Britain’s legalisation of gay marriage has now been put into effect.
The US's John Kerry has likened Uganda's anti-gay legislation to apartheid South Africa.