We present tests of a new method to simultaneously estimate stellar population and emission line (EL) properties of galaxies out of S-PLUS photometry. The technique uses the AlStar code, updated with an empirical prior which greatly improves its ability to estimate ELs using only the survey's 12 bands. The tests compare the output of (noise-perturbed) synthetic photometry of SDSS galaxies to properties derived from previous (STARLIGHT-based) full spectral fitting and detailed EL analysis. For realistic S/N ratios, stellar population properties are recovered to better than 0.2 dex in masses, mean ages, metallicities and +/-0.2 mag for the extinction. More importantly, ELs are recovered remarkably well for a photometric survey. We obtain input minus output dispersions of 0.05-0.2 dex for the equivalent widths of [OII], [OIII], Hbeta, Halpha [NII] and [SII], and even better for lines stronger than ~ 5 A. These excellent results are achieved by combining two empirical facts into a prior which restricts the EL space available for the fits: (1) Because (for the low redshifts explored here) Halpha and [NII] fall in a single narrow band (J0660), their combined equivalent width is always very well recovered, even when [NII]/Ha comes out miserably wrong. (2) We know from previous EL work (eg., with SDSS) that both W(Ha) and W(Ha+[NII]) correlate strongly with [NII]/Ha, which can be used to tell if a galaxy belongs to the left or right wings in the classical BPT diagnostic diagram. These facts are implemented in the code as constraints which act like an empirical prior, resulting in realistic and reliable EL properties. Example applications to integrated light and spatially resolved data are also presented, including a comparison with independent results obtained with MUSE-based integral field spectroscopy.