The Gloggnitzer Bahnhof was also re-built to a design by Wilhelm von Flattich in 1874 (too late for the Weltausstellung), when it was re-named Süd-Bahnhof.
Two railway lines were planned, extending from Vienna to the south and east: one to Wiener Neustadt and Gloggnitz, and one via Bruck an der Leitha to Győr (German: Raab), with an extension to Uj-Szöny (now a suburb of Komárom) and a branch line to Bratislava. This last branch line was, however, never realised.
Initially, the Hungarian lines carried more freight, and were thought to be the more valuable, with plans being proposed to extend the line to Croatia and the Austro-Hungarian port of Trieste. The route to Gloggnitz was stifled by competition from the canal between Vienna and Wiener Neustadt, but benefited from passenger transport to tourist destinations such as Mödling, Gumpoldskirchen, Baden and Bad Vöslau, making it the first Austrian railway to target passenger traffic directly.
According to Matthias Schönerer, who was involved in every major Austrian railway project at the time, rather than a single station, it would be most sensible to build two termini at an obtuse angle to each other. The locomotive factory and other works were to be placed in the space between the two.
The passenger station was built in a classical style, as was usual for public buildings around 1840. The entrance and exit were through the front of the building, which faced the location of the modern Schweizergarten, the station being considerably closer to Südtiroler Platz then than it is now.
The entrance hall was connected to the concourse on the first floor (AmE: second floor) by a staircase. The concourse was the first in Austria, comprised four platforms, large bow windows and was covered by a sturdy 23-metre wide construction of wooden beams held together by iron bands. A house between the two stations served as a restaurant, and was the only building to survive the re-building works on the following 110 years, although the two stations later received separate culinary facilities.
During the boom of the Gründerzeit, a new and larger Südbahnhof was planned by Wilhelm von Flattich, and building was completed in 1874. Including the peripheral wings, the new station was about three times wider than the old one, and the hall was broadened to 35.7 metres (the second largest in Vienna), which was enough for five (later six) platforms. Further platforms for local trains were built to the south of the main hall. The Südbahnhof remained largely unchanged from 1874 to 1945. It served the lines south to Ljubljana, Trieste, Maribor, Carinthia, East Tyrol and Bolzano-Bozen. Until 1914, the CIWL express from St. Petersburg to Cannes stopped there; a remnant of this line, the Vienna-Cannes express continued to travel to and from the Südbahnhof until 1939.
As far back as the time of the Gloggnitzer Bahn, the railway southwards from Vienna was the busiest in the area. It was nationalised in 1924, although the properties remained in the hands of the Donau-Save-Adria-Eisenbahnhn AG until Anschluß in 1938. In contrast to other Viennese stations, the Südbahnhof was relatively undamaged by the Second World War; a small number of bombs fell on it, and a great deal of glass was broken in the fighting in April 1945. The steel framework was largely undamaged and services were soon re-started, although it became clear that renovation works would be necessary.
Following the war, no reason could be found not to unite the two earlier railway stations into a single building. In particular, both railways had come into the ownership of the same company, the ÖBB (Austrian federal railways). The modern Südbahnhof was built between 1955 and 1961 to plans by Heinrich Hrdlicka, in which the twin stations were united in a single building. Two underground platforms serve the S-Bahn network (, , , , , ). At about the same time, the line between Vienna and Gloggnitz was electrified. During the re-building, the Südbahnhof was extended towards the Schweizergarten, while the constituent parts of the old main hall were numbered and taken away to be used at a depot in Floridsdorf.
The interior of the Südbahnhof comprises a large hall with small shops and ticket counters around the edges. Platforms 11–18 (equivalent to the old Ostbahn) are one level higher, and platforms 1–9 (equivalent to the old Südbahn) are two levels above the main hall.
The front of the Südbahnhof is served by tram-lines and . The side entrance on Schweizergartenstraße is served by tram-line and the bus line 13A. The nearest access to the U-Bahn network is a few hundred metres to the east, at Südtiroler Platz.