On the night of June 7, 1893, Mohandas Karamchand Gandhi, a young lawyer, was thrown off the train's first class compartment at Pietermaritzburg station for refusing to give up his seat.
The incident led him to develop his Satyagraha principles of peaceful resistance and mobilise people in South Africa and in India against the discriminatory rules of the British.
The two-day commemoration will commence with a dinner and address by Ms Swaraj and other dignitaries to about 500 guests on June 6, Indian High Commissioner to South Africa, Ruchira Kamboj, said.
The following day about 300 dignitaries, including leading South African politicians, will join Ms Swaraj in a symbolic train ride from Pentrich station to Pietermaritzburg station.
For the event, train coaches and engine will be draped with khadi, a hand-woven fabric synonymous with Mahatma Gandhi, she said.
Making an announcement about the event in Pietermaritzburg yesterday, Ms Kamboj said khadi, which became the symbol of resistance by Mahatma Gandhi against the British rule, would be specially imported from India for the occasion.
The event - the vision of Prime Minister Narendra Modi - would bind South Africa and India which shared the legacy of Mahatma Gandhi.
She said the 125th commemoration was a precursor to Mahatma Gandhi's 150th birth anniversary, for which year-long celebrations were being planned in India from October 2.
She also said the event would be broadcast live in both India and South Africa by countries national public broadcasters, the Doordarshan and the South African Broadcasting Corporation.
Apart from these, the incident of Mahatma Gandhi being thrown off the train on a cold winter evening would be re-enacted, and his a two-sided bust would be installed on the station platform.
"One side of the bust will feature Mahatma Gandhi as a lawyer in the Western attire he wore when he came to South Africa, while the other side will show Mahatma Gandhi in his Indian dress in which he left South Africa after 21 years, returning to transform India " Ms Kamboj said.
An interactive digital museum, sponsored by the Indian government, will also be launched at the station on the day, she added.