Yes. PQRS must also be reported in order to avoid the non-reporting penalty. PQRS and Meaningful Use are separate CMS programs.
Beginning in 2017, with the introduction of MIPS, Meaningful Use will be replaced by a component called Advancing Care Information or ACI. Reporting ACI will have the potential of earning the provider/practice up to 25 points in their overall composite score. ACI can be attested to via MDinteractive.