Ahmed Awad bin Mubarak was handed over to a delegation of tribal leaders.
He was meant to be released last week as part of a deal agreed with President Abdrabbuh Mansour Hadi to end a violent stand-off in the capital, Sanaa.
Mr Hadi and his government have since offered their resignations, saying they could not continue in their posts under such pressure from the rebels.
Their decision came after the Houthis seized the presidential palace complex and shelled the president's private home.
In a televised speech following the release of Mr Hadi's chief of staff, rebel leader Abdul Malik al-Houthi dismissed the president's resignation as a "manoeuvre".
He said Yemeni political parties, with UN support, had been holding consultations.
"We are seeking a peaceful transfer of power on the basis of partnership," he was quoted by the Reuters news agency as saying.
The resolutions of the National Dialogue Conference (NDC), held after an uprising forced longtime President Ali Abdullah Saleh from power, and the peace deal signed by Mr Hadi after the rebels overran Sanaa in September, would be the basis for any agreement, he added.
"Let everyone go towards co-operation instead of clashing, arguing and wrestling."
A week ago, Mr Houthi accused the president and those around him of failing to implement political deals which he said should have ushered in a new era in Yemen.
He listed as his main demand the shake-up of the commission tasked with writing a review of a new constitution to ensure more representation for his group.
The rebels have rejected a draft of the charter that would create a federal state of six regions, even though the plan was a recommendation of the NDC, which they backed.
They seized Mr Bin Mubarak on 17 January to stop him attending a meeting to discuss the draft, saying they had become aware of "irregularities" in the text.
Shia Houthi rebels in Yemen have freed a senior presidential aide who they abducted 10 days ago.