Aims: Whereas the evolution of gas kinematics of massive galaxies is now relatively well established up to redshift z ~ 3, little is known about the kinematics of lower mass (M⋆≤ 1010M⊙) galaxies. We use MUSE, a powerful wide-field, optical integral-field spectrograph (IFS) recently mounted on the VLT, to characterize this galaxy population at intermediate redshift. Methods: We made use of the deepest MUSE observations performed so far on the Hubble Deep Field South (HDFS). This data cube, resulting from 27 h of integration time, covers a one arcmin2 field of view at an unprecedented depth (with a 1σ emission-line surface brightness limit of 1 × 10-19 erg s-1 cm-2 arcsec-2) and a final spatial resolution of ≈0.7''. We identified a sample of 28 resolved emission-line galaxies, extending over an area that is at least twice the seeing disk, spread over a redshift interval of 0.2