Zeidan accused the Justice and Construction Party -- the political arm of the Libyan branch of the Muslim Brotherhood that has been bloodily repressed in neighbouring Egypt since the ouster of elected president Mohamed Morsi -- of seeking to destabilise his government.
The resignation of the five ministers came after three weeks of wrangling over an Islamist-inspired censure motion against the premier.
The Islamists failed to secure the required 120 votes in the 194-member General National Congress to pass the motion. and 99 members signed a petition of protest earlier today.
Zeidan has said repeatedly that he will quit only when there is consensus on a successor to avoid a power vacuum in the midst of the mounting insecurity gripping large swathes of the country two and a half years after the overthrow of veteran dictator Moamer Kadhafi.
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Earlier this month, the premier said he would soon announce a major cabinet reshuffle, something he promised to do repeatedly last summer without ever taking action.
The JCP said it was "withdrawing its ministers from Zeidan's government and holds those in the Congress who backed his government responsible."
Zeidan was "incapable of taking the country where it needs to go," the party said.
The party has five ministers in Libya's 32-member interim administration -- those for oil, electricity, housing, economy and sport.
Earlier, 99 MPs, including those of the JCP, signed a petition of protest accusing Zeidan of a "crushing failure" in his efforts to assert central government control over former rebel militias that operate with virtual impunity across much of the country.