Interannual/decadal variability in the sea surface temperature at the south subtropical Indian Ocean plays a crucial modulator in the regional climate. The south Indian Ocean dipole mode is one of the dominant modes of such variability. Using a high-resolution global model simulation, we show that internal oceanic variability is one of the primary causes of this observed low-frequency variability in this region. The instability embedded into the large-scale Rossby waves propagates across the south subtropical Indian Ocean, modulating the position and strength of the South Equatorial Current and the South Indian Counter Current. In the process, these current systems impact the thermocline, sea surface height, and the surface temperature of this basin. We further show that the preferential frequency of variability driven by these internal oceanic variabilities is determined by the time these embedded instabilities in large-scale Rosby waves take to cross the longitudinal extent of the south tropical basin.