Context. We study the peculiar interacting galaxy system of VCC 1249/M49 located in the core of the Virgo B subcluster. Owing to a recent interaction between the dwarf galaxy VCC 1249 and the halo gas of the elliptical galaxy M49, neutral hydrogen has been displaced from the interstellar medium of this dwarf into the Virgo intracluster medium. Observations also reveal multiple compact star-forming regions (aka H II regions) that are embedded in this H I cloud, with a projected separation up to 13 kpc from VCC 1249 in the northwest direction. Aims. Motivated by recent near-ultraviolet imaging from the GALEX Ultraviolet Virgo Cluster Survey (GUViCS) of the VCC 1249/M49 system that shows significant ongoing/recent star formation in the compact regions, we aim to constrain the origin of these outlying H II regions with a multi-wavelength approach. Methods. Using deep optical (u, g, i, z) imaging from the Next Generation Virgo Cluster Survey (NGVS) and new Ha imaging obtained at the San Pedro Martir observatory together with Keck long-slit spectroscopy, we characterize the star formation rates, ages, and metallicity of VCC 1249 and its outlying compact regions. Moreover, we analyze the color and luminosity profile of the galaxy to investigate its recent interaction with M49. Results. Our new observations indicate that VCC 1249 underwent a recent interaction with M 49 in which both ram-pressure stripping and tidal interaction occured. The joint action of the two mechanisms led to the removal of the Hi gas from the interstellar medium of VCC 1249, while the gravitational tides triggered the stellar tail and counter-tail of VCC 1249. Our stellar population synthesis analysis reveals that the star formation in this galaxy was truncated around 200 Myr ago and that the outlying H II regions were born in situ approximate to 10 Myr ago out of pre-enriched gas removed from the dwarf galaxy. These observations also reveal that interactions between central and satellite galaxies similar to those between VCC 1249/M49 may be an effective way of dispersing metals into the halos of massive galaxies.