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Jupiter's South Polar Region (SPR) was observed by James Webb Space Telescope/Mid‐Infrared Instrument in December 2022. We used the Medium Resolution Spectrometer mode to provide new information about Jupiter's South Polar stratosphere. The southern auroral region was visible and influenced the atmosphere in several ways: (a) In the interior of the southern auroral oval, we retrieved peak temperatures at two distinct pressure levels near 0.01 and 1 mbar, with warmer temperatures with respect to non‐auroral regions of 12 ± 2 K and 37 ± 4 K respectively. A cold polar vortex is centered at 65°S at 10 mbar. (b) We found that the homopause is elevated to 590−118+25 ${590}_{-118}^{+25}$ km above the 1‐bar pressure level inside the auroral oval compared to 460−50+60 ${460}_{-50}^{+60}$ km at neighboring latitudes and with an upper altitude of 350 km in regions not affected by auroral precipitation. (c) The retrieved abundance of C2H2 shows an increase within the auroral oval, and it exhibits high abundances throughout the polar region. The retrieved abundance of C2H6 increases toward the pole, without being localized in the auroral oval, in contrast with previous analysis (Sinclair et al., 2018, https://doi.org/10.1016/j.icarus.2017.09.016). We determined that the warming at 0.01 mbar and the elevated homopause might be caused by the flux of charged particles depositing their energy in the SPR. The 1‐mbar hotspot may arise from adiabatic heating resulting from auroral‐driven downwelling. The cold region at 10 mbar may be caused by radiative cooling by stratospheric aerosols. The differences in spatial distribution seem to indicate that the hydrocarbons analyzed are affected differently by auroral precipitation. Plain Language Summary: James Webb Space Telescope/Mid‐Infrared instrument observed Jupiter's south polar region in December 2022. The instrument acquired spectroscopic data in the mid‐infrared part of the spectrum, which is sensitive to the temperature of the atmosphere and the chemical abundances. These observations revealed that within the auroral oval there are two regions of high temperatures located at two different altitudes. These are presumably caused by two different phenomena: direct heating from the incoming charged particles in the aurora at a height of 0.01 mbar and adiabatic heating in downdrafts at lower levels. A decrease in temperature was also observed as we approached the South Pole, probably caused by a cold polar vortex associated with stratospheric hazes. We found that the altitude of the homopause (the limit between the well‐mixed part of the atmosphere and the part where molecules are separated according their specific weight) is altered by the auroras, being up to 100 km higher in the auroral region. The atmospheric abundances of acetylene and ethane showed an enrichment of acetylene within the auroral oval, and of ethane at the pole, which may indicate that these molecules are not affected in the same way by the energy input of the aurora. Key Points: The homopause is spatially variable within the polar region and highest within the auroral ovalThe atmosphere inside the Southern Auroral Oval at 1 and 0.01 mbar shows a warming compared with non‐auroral regionsThe C2H2 abundance is enhanced inside the Southern Auroral Oval at 0.1 and 7 mbar, and C2H6 shows an increase polewards [ABSTRACT FROM AUTHOR]