We report the detection of extended Ly alpha emission around individual star-forming galaxies at redshifts z = 3-6 in an ultradeep exposure of the Hubble Deep Field South obtained with MUSE on the ESO-VLT. The data reach a limiting surface brightness (1sigma) of ~1 x 10^-19 erg s^-1 cm^-2 arcsec^-2 in azimuthally averaged radial profiles, an order of magnitude improvement over previous narrowband imaging. Our sample consists of 26 spectroscopically confirmed Ly alpha-emitting, but mostly continuum-faint (m_AB >~ 27) galaxies. In most objects the Ly alpha emission is considerably more extended than the UV continuum light. While 5 of the faintest galaxies in the sample show no significantly detected Ly alpha haloes, the derived upper limits suggest that this is just due to insufficient S/N. Ly alpha haloes therefore appear to be (nearly) ubiquitous even for low-mass (~10^8-10^9 M_sun) star-forming galaxies at z>3. We decompose the Ly alpha emission of each object into a compact `continuum-like and an extended halo component, and infer sizes and luminosities of the haloes. The extended Ly alpha emission approximately follows an exponential surface brightness distribution with a scale length of a few kpc. While these haloes are thus quite modest in terms of their absolute sizes, they are larger by a factor of 5-15 than the corresponding rest-frame UV continuum sources as seen by HST. They are also much more extended, by a factor ~5, than Ly alpha haloes around low-redshift star-forming galaxies. Between ~40% and >90% of the observed Ly alpha flux comes from the extended halo component, with no obvious correlation of this fraction with either the absolute or the relative size of the Ly alpha halo. Our observations provide direct insights into the spatial distribution of at least partly neutral gas residing in the circumgalactic medium of low to intermediate mass galaxies at z > 3.