In a statement adopted by the 15 members, the council said Hadi "is the legitimate authority" and "all parties and political actors in Yemen must stand with President Hadi, Prime Minister (Khalid) Bahah, and Yemen’s cabinet to keep the country on track to stability and security."
The Shiite militia fighters known as the Huthis earlier attacked the presidential complex and Hadi's residence in an apparent bid to overthrow the embattled government.
Hadi's government has been a key ally of the United States, allowing Washington to carry out repeated drone attacks on Al-Qaeda militants on its territory.
The council called for a full ceasefire and a return to dialogue to resolve differences, but there was no threat of sanctions.
UN special envoy Jamal Benomar was headed to Sanaa from Doha after briefing council members by videolink.
Benomar told the council that the Huthi fighters had launched a "massive attack using heavy weapons" on the palace, a diplomat present at the closed meeting said.
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The Moroccan diplomat has been leading negotiations on forming a unity government in Yemen but faces resistance from the Huthis, who have tightened their control over Sanaa since they overran the capital in September.
Secretary General Ban Ki-moon said he was "gravely concerned" and called on armed factions to stop fighting immediately.
On the attack on the presidential palace, the security council said it "rejected such violent efforts to undermine or interfere with Yemen's legitimate government institutions."
It also welcomed a draft constitution and said the new power-sharing document should be finalized rapidly in a manner that meets the aspirations of the Yemeni people.
In a televised address, Huthi leader Abdul Malik al-Huthi shrugged off possible UN measures against his movement and asserted: "We are ready to face the consequences, regardless of what they are."
The council in November imposed sanctions on former president Ali Abdullah Saleh and two allied Huthi commanders for threatening peace in the impoverished Arab country.
Saleh has been accused of backing the Huthis and a source in the presidential guard told AFP some Yemeni troops still loyal to the ex-leader had supported the militia in the latest fighting.