How tectonic plate motions are coupled with mantle flows remains an open question. Quasi-periodic 2000 km wavelength undulations aligned with absolute plate motion in the Pacific and Indian Ocean basins, observed in gravity and seafloor topography and coinciding with seismically imaged low shear velocity fingers in the upper mantle, suggest the presence of meso‑scale convection below the lithosphere. However, the correspondence of sub-lithospheric mantle mass excess, seafloor lows and slow upper mantle seismic velocities cannot be explained by temperature variations alone. Here we introduce a simplified system of bi-dimensional convective cells of width ∼1000 km, extending from the base of the lithosphere through the extended mantle transition zone (down to 1000 km depth), at least partly driven from below. From mass balance considerations in a viscous Earth, we show that the density excess required in the hot upwelling limbs may reflect the formation of stable dense lenses of dehydration-induced partial melt atop the 410 km discontinuity, and upward entrainment of a small fraction of quasi-buoyant partially molten and recrystallized material across the upper mantle. Our model provides an explanation for the thin low shear velocity layer detected intermittently above the 410 km discontinuity in some parts of ocean basins away from subducted slabs, and supports the presence of water in the transition zone.