King Mohammed VI had been unaware of the gravity of the Spaniard’s crimes, his cabinet said earlier.
Protesters had threatened fresh rallies in Rabat and Casablanca next week.
Daniel Galvan Vina, believed to be in his sixties, was sentenced to 30 years in prison in September 2011.
However, last week he was freed by royal decree from a jail in Kenitra, north of the capital. He is reported to have left the country.
The king “has decided to withdraw the pardon previously accorded to Daniel Galvan Vina”, the palace said in a statement carried by the official Map news agency.
The Ministry of Justice said it would discuss “the next step” with regards to the Spaniard, the agency reported.
Dozens of people were injured in violent confrontations between hundreds of protesters and police outside parliament in the Moroccan capital on Friday.
Demonstrations were also reported in the cities of Kenitra, Tangier and Tetouan, as well as outside the Moroccan embassy in Paris.
“The king was never informed – in any way or at any time – of the seriousness of the abject crimes of which the person concerned was convicted,” a statement released by the royal palace said on Sunday.
“It is clear that the sovereign would never have consented” to his release, given the “monstrous crimes” committed, the statement concluded.
It is normal procedure for the king to pardon prisoners on special occasions, such as Throne Day, last Tuesday.
Morocco’s Justice Ministry said on Friday the pardons were based on national interests and “friendly relations” with Spain.
A number of foreign nationals have recently been detained in Morocco under suspicion of pedophilia.
In June, a British man was arrested in the port town of Tetouan over allegations of raping a six-year-old girl. In May, a Casablanca court sentenced a French man to 12 years in jail on hemophilia charges.
Thousands of Moroccans marched in Casablanca earlier this year to condemn pedophilia and violence against children in the north African country.