The young migrants forced their way through the high border fence into the Spanish North African territory, ecstatic to have finally crossed into a European Union state.
Some kissed the ground and shouted "Thank you lord" and "Viva Espana", although several had bloodied hands and feet as well as torn clothes after making it through the barrier.
Ceuta and Melilla, also a Spanish territory in North Africa, have the EU's only land borders with Africa.
"356 managed to get in out of a total of around 700" who attempted entry, a spokesman for the local authority said. "They entered after breaking access gates with shears and hammers."
Their arrival came just days after nearly 500 migrants crossed into Ceuta on Friday, one of the biggest breaches since the border barrier was reinforced in 2005.
The Spanish territory is now ringed by a double wire fence eight kilometres (five miles) long. The six-metre high fence also has rolls of barbed wire.
"We took 11 people to hospital, eight needed stitches and three needed an X-ray," she said.
The border rush also comes amid a dispute between Morocco and the EU over the interpretation of a free trade farm and fishing deal.
Ties between Morocco and Brussels suffered a blow last year after an EU tribunal annulled the deal on the grounds it illegally applied to the Western Sahara, a former Spanish colony controlled by Rabat.
The Algeria-backed Polisario Front has long been fighting for independence for the region and had challenged the agreement.
Earlier this month, Rabat warned Brussels that failure to implement the deal would have severe consequences and could spur illegal migration as it would affect "thousands of jobs" in Morocco and in Europe.
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