John Oster had a chance to level as Reading looked to respond but saw his header tipped away before Michael Owen hooked Habib Beye's cross into the net.
Shearer expressed concern that Newcastle would struggle on the pitch in the Championship unless the team's off-field problems were swiftly rectified, allowing a new manager to strengthen a squad whose departures have included Michael Owen, Obafemi Martins, Mark Viduka, Habib Beye and Sebastien Bassong.