I am flying to South Africa in few days. I have a valid short-term visa (20 days) . I saw this just now http://www.vfsglobal.com/southafrica/india/conferences.html and below that http://www.vfsglobal.com/southafrica/india/pdf/Medical_form_301214.pdf . I swear I didn't see this before, it wasn't there, probably has come after 1st June 2016. Now is it imperative that I get this filled by a physician and could I be denied entry at the airport (either in CPT,SA or in India before boarding the aircraft) ?
That form appears to only be required for other types of visas.
On the page for short-term visas for "conferences," the "documents required" tab lists the documents you needed to submit. It does not list a medical report. In contrast, the page for a long-term study visa does state that both a medical report and a radiological report (to confirm that you don't have TB) are required.
We can also consult Timatic, the system the airline will use to determine what documents are required. It states that a visa is required, which you already have, but does not indicate any medical form is needed. The only health-related requirement is that "Passengers who have visited Guinea, Liberia or Sierra Leone are subject to screening and health checks."