In 1924, historian John Cooper noted that when the South Yarra to Oakleigh line was first constructed, a set of points connected the line to the existing Brighton line. However, a high embankment obscured the vision of train drivers approaching South Yarra on both lines. To solve that problem, it was decided that the Oakleigh line should have its own tracks into Melbourne, and the Cremorne Railway Bridge, spanning the Yarra River, was duplicated to allow that.[7]
The opening of the South Yarra to Oakleigh line in 1879 made the proposed Outer Circle line largely redundant, but it was constructed anyway, a decade later.
In 1946, the current Cremorne Railway Bridge over the Yarra River was opened, replacing the earlier one.[6] In 1947, a works siding opened, which was disconnected in 1955.[6]
Even after the laying of six tracks from Richmond to South Yarra, and the abolition of the signal box, the station retained three emergency crossovers at the up end of Platforms 1 and 2, 3 and 4 and 5 and 6. The latter set was removed in 1983, followed by the middle pair by 23 June 1984,[9] and the final set in August 1986.[10] The crossovers were originally provided in 1945 and 1960.[6] Also in 1960, the "local lines", used by Pakenham and Cranbourne line services, were extended to Richmond, and the signal box, located at the up end of Platforms 4 and 5, was closed,[6] but still remains in place.
In 1993, there were major re-signalling works between South Yarra and Toorak,[6] with similar works occurring between South Yarra and Richmond in 1994.[6] In 1997, South Yarra was upgraded to a premium station.[11] As such, the station is staffed from the first to the last service each day.
In early 2020, it was announced that South Yarra was to undergo a $12 million refurbishment. The entrance to the station on Toorak Road was to be widened, and the layout changed to make the station larger.[14][15]
Services on the Pakenham and Cranbourne lines will no longer stop at South Yarra when the Metro Tunnel opens, which is scheduled to take place in 2025. The entrance portal to the Metro Tunnel is located near the station, but South Yarra will not be integrated into the new tunnel, which generated some criticism.[16][17]