The surge, which began on Thursday at one of the EU's only two land borders with Africa - the other being Morocco's frontier with the Spanish enclave of Melilla - triggered alarm across the bloc.
Migration has been one of the European Union's most divisive political issues since the 2015-16 migration crisis, when more than one million refugees and migrants, many fleeing war in Syria, arrived in Europe.
The influx fuelled support for anti-immigration and far-right parties across the bloc and intensified years of disputes over border controls, asylum rules and burden-sharing. Increasingly, the EU relies on migration agreements with countries in North Africa to curb irregular arrivals.
"Morocco is an important strategic partner, particularly in our efforts to combat migrant smuggling and illegal migration," European Commission President Ursula von der Leyen wrote.
"In co-operation with Spain, especially on anything related to Ceuta and Melilla, we could enhance border management early-warning systems and improve our technical and financial support to Morocco."
Morocco on Sunday said recent mass crossings to Ceuta and Melilla had been fuelled by misinformation on social media, human trafficking networks and misinterpretation of a Spanish court ruling.
In the event, most of those who breached the border barrier found no food or welcome, and returned to Moroccan soil.
Nevertheless, Italy suspended passport-free Schengen travel arrangements with Spain for a month, even though they do not apply to Ceuta, while 22 of the EU's 27 members urged coordinated action to strengthen the bloc's external borders.
The Ceuta incident is the first major test of the EU's Migration Pact, which entered into force in June after years of negotiations aimed at creating common migration rules and stronger solidarity among member states.
"The idea of the pact is control and solidarity between EU member states. Yet we've seen the opposite," said Bram Frouws, director of the Mixed Migration Centre.
"If the first major incident shows that the pact isn't doing much differently, that's politically risky," he said, arguing it could undermine confidence in European leaders and provide "fuel for the far right".
With elections approaching in several EU countries, migration remains among the bloc's most politically sensitive issues.
Critics argue the strategy of relying on transit countries leaves Europe vulnerable to pressure if these relax migration controls, or threaten to do so, in pursuit of political or economic concessions.
"Europe's increasing reliance on neighbouring countries for migration control may reduce arrivals in the short term, but it can also provide those countries with significant political leverage," said Alberto-Horst Neidhardt, senior policy analyst at the European Policy Centre.
