The seeds of this conflict were sown in colonial times and the roots extend to World War 1.
German South West Africa (Deutsch-Südwestafrika) was a German colony from 1884. the Brittish empire that had annexed the Cape colony from the dutch also annexed the main South West Africa port , Walvis Bay in 1878, and incorperated it into the Cape Colony in 1884.
With World War 1 starting in Europe, the then Union of South Africa was very aware of the bordering German colony.
A first attempt to invade German South West Africa from the south failed at the Battle of Sandfontein, close to the border with the Cape Colony, where on 26 September 1914 the German fusiliers inflicted a serious defeat on the British troops, although the survivors were left free to return to British territory.
After having to deal with a insurrection at home, from Boers sympathetic to the German cause, a two pronged attack was launched on the German colony from the south and from Walvis Bay.
By Eduard Rothert (1839-1916) - Eduard Rothert, Karten und Skizzen zum Weltkrieg, Druck und Verlag von A. Bagel, Düsseldorf, 1916.Originally uploaded to EN Wikipedia by Victor_falk 31 July 2007, Public Domain, Link
Germany forces soon surrendered and the war was over by mid 1915.
South African casualties were 113 killed, 153 died of injury or illness and 263 wounded. German casualties were 103 killed, 890 taken prisoner, 37 field guns and 22 machine-guns captured.
South Africa administered South West Africa as a League of Nations mandate territory from 1919 until World War 2.
The Mandate was supposed to become a United Nations Trust Territory when League of Nations Mandates were transferred to the United Nations following the Second World War. The Prime Minister, Jan Smuts, objected to South West Africa coming under UN control and refused to allow the territory's transition to independence, instead seeking to make it South Africa's fifth province in 1946.
They never formally annexed the territory but administered it as a fifth province and pretty much had no plans of giving the territory back or allowing for independence or self rule.
Once the newly created independent South Africa (no longer British controlled Union of South Africa)began extending their Apartheid policies to this territory in 1948 it fueled the desires for independence of the majority black population in the North.
A number of nationalist organizations sprang up culminating in SWAPO the South West Africa People's Organization.
The Old Location Massacre that took place in December, 1959, carried out by South Africa military force, was the major turning point. After the massacre, the SWAPO's leadership came to realize that their approach to the oppressor had little impact. In 1960 majority of SWAPO senior leaders went into exile and started to loby for military support. This led to the establishment of an armed wing, known as the South West Africa Liberation Army (SWALA), an armed insurgency immediately began.
SWALA was renamed to PLAN in 1966.
Initial military training occurred in Egypt and Algeria. Recruits were trained in camps in Zambia.
The first clashes were on 26 August 1966 which is generally regarded as the start of the South African Border War. From then onward PLAN launched incursions from Zambia and eventually Angola.
Source : various relevant Wikipedia pages