The Phase-2 upgrade of the CMS detector for the high luminosity era of the LHC (HL-LHC) foresees the installation of a new tracking system to cope with the increased pileup and track multiplicity. The inner layers of the outer tracker will be equipped with pixel-strip modules that have a fine segmentation to provide an accurate position measurement. Each module contains two types of silicon sensors, a strip and a macro-pixel sensor. The pixelated sensor and its readout chip together form the macro-pixel sub-assembly, or MaPSA. A rigorous quality control procedure for the MaPSAs has been developed and validated using prototype assemblies. This report describes the qualification setup and procedure, as well as the results of measurements on the prototypes.