In his letter of resignation Hadi, a key US ally in the fight against Al-Qaeda, said he could no longer stay in office as the country was in "total deadlock".
"I believe that I have not been able to achieve the goals for which I took up my duties," he said, adding that Yemen's political leaders had failed "to lead the country to calmer waters".
Prime Minister Khalid Bahah also tendered his resignation, saying he did want to be part of the collapse of the country.
"Parliament... Refused to accept the president's resignation and decided to call an extraordinary session for today morning," the official said, speaking on condition of anonymity.
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The shock announcements came after the militia, known as Huthis, tightened their grip on Sanaa this week after seizing almost full control of the capital in September.
They had maintained fighters around key buildings on yesterday and continued holding a top presidential aide they kidnapped on Saturday, despite a deal to end what authorities called a coup attempt.
The potential fall of Hadi's Western-backed government will raise serious concerns of strategically important but impoverished Yemen collapsing into complete chaos.
AQAP is considered Al-Qaeda's most dangerous affiliate and claimed responsibility for this month's deadly attack on French satirical weekly Charlie Hebdo.
Yemen has allowed the United States to carry out repeated drone attacks on Al-Qaeda militants in its territory.
Hadi is from Yemen's formerly independent south and in recent days southern officials have taken steps to back his rule, including closing the air and sea ports in main city Aden.
The security and military committee for four of south Yemen's provinces, including Aden, said in a statement yesterday it would not take orders from Sanaa following Hadi's resignation.
"Our team is seeking confirmation of all of the reports," Psaki told reporters.