The Spanish government's representative in Ceuta said 57 bodies had been recovered on the Spanish side of the border and that there could be additional casualties on the Moroccan side.
It said some drowned and some were crushed while trying to climb the breakwater that holds the border fence.
Spain's interior ministry said about 50,000 people had crossed the border since Thursday morning, and estimated that 48,300 had returned by 6pm on Friday.
Juan Jesus Vivas, head of Ceuta's local government, said as many as 60,000 people had pushed across over the past couple of days.
Moroccan forces beat back crowds with batons and tear gas at the gates to Ceuta, trying to prevent more from entering the tiny Spanish territory that juts on a spit of sandy land into the Mediterranean from Morocco.
The rush on the border caused division in Europe, where leaders of fellow European Union countries called for Spain to ensure that the incident was contained.
Italy said it was suspending the EU's border-free Schengen arrangements with Spain, a measure set to affect people travelling by plane or boat between the two countries.
Spain said the move violated EU treaties.
French Interior Minister Laurent Nunez said the police presence on the France-Spain border would be quintupled by Saturday while reinforcing aerial surveillance and patrols on trains.
US President Donald Trump told a cabinet meeting the Ceuta crossings "look like an invasion," adding: "That same thing's going to happen to us if the Republicans don't get elected, except worse," referring to upcoming midterm elections.
EU countries are normally barred from conducting checks at internal frontiers of the bloc's Schengen zone, although checks can be reimposed temporarily under exceptional circumstances.
Moroccan police in riot gear used tear gas at the enclave's border to disperse some of the people amassed near the fences.
Water cannon trucks were deployed and the charred remains of a bus and seven cars could be seen from clashes with the crowds.
On the other side, Spanish military vehicles lined up along sections of the border as dozens of migrants watched from a hilltop in Morocco, unable to cross.
Several hundred people could be seen returning to Morocco through border posts and holes in the fence, with some saying they could not find food or shelter in Ceuta.
"Honestly, I don't even know why I came, and now I'm going back," a young Moroccan man, who said he was from Tangier, told Reuters.
"I haven't eaten since lunch yesterday, even though I brought some money with me ... What we're doing is neither good nor enjoyable."
Ayman, a 20-year-old hairdresser from the port city of Larache who only gave one name, told Reuters he had crossed on Wednesday after a five-hour swim.
"There was no food inside Ceuta and we were kicked out badly by the (Spanish) army," he said.
Spanish Prime Minister Pedro Sanchez travelled to Ceuta on Friday, where he was greeted with insults from protesters.
He called the mass crossing "a violation of Spain's territorial sovereignty" and said authorities were speeding up the repatriation of those who had entered illegally, with full co-operation from Morocco.
Ceuta and Melilla, Spanish autonomous cities in northern Morocco, have the EU's only land borders with Africa.
Both periodically experience surges in attempted crossings by migrants seeking to reach Europe but the scale of Thursday's rush appeared unprecedented.
In a post on X, Spain's Guardia Civil police association AUGC said there had been too few police in place to monitor the fence during the surge on Thursday, making them unable to stop the rush.
