Morocco striker Khalid Boutaib gave the north African side a shock early lead but Isco levelled, blasting high into the net after a layoff from Andres Iniesta.
Morocco, already eliminated, struck again in the 81st minute when substitute Youssef En-Nesyri crashed in a header which looked set to inflict a first defeat on Spain since Euro 2016.
But substitute Iago Aspas levelled in stoppage-time after consultation from the video assistant referee (VAR), putting Spain top ahead of Portugal, who were held to a 1-1 draw by Iran.
Spain will play Russia in the last 16.
