The loss comes after fighters backing a rival administration in east Libya seized two other terminals from guards loyal to the Tripoli-based Government of National Accord (GNA) on Sunday.
All three Mediterranean ports are in Libya's "oil crescent", an area seen as a vital source of income for the GNA, which has struggled to assert its authority across the country.
"Our armed forces were able to take control of Zuwaytina port and secure it completely," a spokesman for the fighters that took the terminals said.
The LANA news agency loyal to the eastern administration reported a military source as saying: "The armed forces are now concentrated at the port and have secured it after expelling outlaw militia from it."
The forces are commanded by controversial general Khalifa Haftar, who has refused to back the GNA and supports the parallel authority based in east Libya.
On Sunday they took the Al-Sidra and Ras Lanuf ports before attacking Zuwaytina to the east.
It is the first time that Haftar's forces and fighters loyal to the GNA have clashed directly since the unity government started working in the capital in March.
- 'Critical juncture' -
The unity government called on all forces loyal to it to "protect and defend" the ports against what it called "flagrant aggression" against Libyan sovereignty.
It warned overnight that the country was at a "critical juncture", adding "the hopes of Libyans for stability in the country have been dashed".
The head of the rival government in the eastern city of Bayda said it would work on reopening the ports as soon as possible.
"We will work on the oil ports resuming work as soon as possible so as to guarantee all Libyans a decent life," Abdullah al-Thani said.
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Haftar's forces said they would hand over the management of the ports to the National Oil Corporation (NOC) to resume oil exports.
The NOC is split into two rival branches, one allied to the GNA and the other to the administration that Haftar supports.
Oil is Libya's main natural resource with reserves estimated at 48 billion barrels, the largest in Africa.
But since 2010 the country's production has plummeted from 1.5 million bpd to just 200,000 bpd.
The seizure of the ports deals a heavy blow to the unity government, depriving it of a key source of income.
In late July, the GNA agreed to resume oil exports out of Ras Lanuf and Al-Sidra -- which together have a capacity of 700,000 barrels of oil per day -- after months-long closure following jihadist attacks.
They shut after attacks in January by the Islamic State group, who have gained a foothold in the country.
- Rival authorities, militia -
Libya has been in chaos since the 2011 uprising that toppled and killed longtime dictator Moamer Kadhafi, with rival authorities and militia vying for control.
The port of Brega -- between Ras Lanuf and Zuwaytina -- remains in the hands of the oil installation guards.
A spokesman for Haftar's forces, Colonel Mohammad Mesmari, told the press late Sunday that efforts were underway to seize the port without fighting.
Analyst Mattia Toaldo said Haftar's assault on the oil ports looked to take advantage of the exhaustion of pro-GNA forces after battling IS.
Once pro-GNA forces expel IS from its coastal stronghold city of Sirte and there is no buffer between them and Haftar's army, either side "could easily clash again," Toaldo said.
But Michael Nayebi-Oskoui, a senior analyst at the Statfor intelligence group, said he didn't think a direct confrontation between Haftar's fighters and pro-GNA forces was probable.
"I don't think the GNA is looking to get into a fight it likely won't win," he said.