First, Morales stroked home a penalty on 12 minutes after Roman Torres was penalised for handling inside the visitors' box.
Seven minutes later, it was two when Morales's inch-perfect cross was met by Jaime, who powered his header past Stefan Frei to put Real in cruise control.
However, the hosts were millimetres from reducing the deficit 10 minutes before the break when Obafemi Martins's effort cannoned off the crossbar.
After the break, Morales and Luis Silva went close, with the latter missing from a matter of yards shortly after the hour mark.
Torres should have reduced the arrears in the final six minutes but his header was comfortably dealt with by Rimando as the hosts held on for a clean sheet.