There are no direct flights that can be taken from India to Johannesburg, which is the nearest airport to Pretoria. Several connecting flights however run from the major international airports in India. Most of these have one stopover, some even two. Airlines like Ehtiopian Airlines, Jet Airways, Kenya Airlines, South African Airlines, Qatar Airways and several others provide services along these routes.
The closest airport to Pretoria is in Johannesburg, the OR Tambo International Airport. From there you can take a taxi, or take the Metrorail from Isando which will take another hour to take you to Pretoria.
The N1, N3, N4, N14 national highways connect with several regional highways to make Pretoria accessible from pretty much every part of South Africa via car
The Gautrain and the Metrorail connect Pretoria to cities all over Gauteng inlcuding Centurion, Midran, Johannesburg and others.
Many major bus companies like Intercape, Greyhound, Translux and the backpacker hop on-hop off BazBus connect Pretoria to all major South African cities.