This paper describes a method to automatically and reproducibly inject sharply delimited sample plugs in the shallow (i.e., sub-micron) channels typically used in shear driven chromatography. The formation of asymmetric plugs, which typically occurs during loading of the sample in wide channels, is circumvented by etching a slit in the middle of the channel that is connected to a micro-well and a vacuum system with syringes for the supply of both the analyte and the mobile phase. The design of the injection slit was supported by a series of CFD simulations to optimize its shape and that of the corresponding injection well. The system was intensively tested experimentally and showed good reproducibility, both for the width and the area of the injected peaks (relative standard deviations are max. 4 and 6%, respectively). The concentration of the injected plug was found to be approximately 80% of the original sample concentration. It was also observed that with the current setup the lower limit of the peak width was about 120 mu m. This is a consequence of the fact that the peak width originating from the convection filling step becomes negligible to the contribution of diffusion during the filling and flushing time. Being fully automated and perfectly closed, the presently proposed injection system also paves the way to integrate other functionalities in shear driven chromatography, i.e. gradient elution and parallelization.