The home side had to withstand some early pressure in the opening stages and they might have been behind had it not been for the brilliance of David de Gea, who reacted well to keep out Darko Velkoski's point-blank header.
It was the visitors who continued to cause problems in the early minutes and Macedonia came close again, this time through Goran Pandev who moved quickly to flash a header just beyond the post with the Spanish defence scrambling.
The visitors appeared to be coping well with some growing Spanish pressure, but they suffered at the hands of an unfortunate error when Darko Velkoski headed into his own net in the 34th minute.
The first goal seemed to inspire Spain into action and they came out of the traps quickest in the second period, Morata almost earning himself a goal with a fine strike, only to be denied by the dive of Dimitrievski down low.
The all-important second goal arrived in the 63rd minute and it was no more than the hosts deserved, as Victor Vitolo reacted quickest to a rebound before producing a standout bullet header beyond the reach of the Macedonian keeper.
Spain were able to add some icing to the cake six minutes from time, as Nacho Monreal and Aritz Aduriz added late efforts in order to leave La Roja with 10 points from four games at the summit of their group.