But that alliance unravelled over the past week as the former leader reached out to the Saudi-led coalition that has waged an air campaign against the Houthis since March 2015.
Things came to a head on Monday when Saleh was killed in a roadside attack by members of the Shiite militant movement. He called for his father's backers to "take back Yemen from the Iranian Houthi militias".
Houthi rebels in Yemen have held dozens of journalists captive for days at a television station in the capital and a media watchdog has demanded their immediate release. "He got what he deserved", Ali Akbar Velayati, an aide to Iran's supreme leader, was quoted as saying by the semi-official Tasnim news agency.
In a televised speech, Yemeni President Abd-Rabbu Mansour Hadi called on Yemenis to rise up against the Iran-aligned Houthis.
Fierce clashes broke out in Sanaa last week between Saleh supporters and the Iran-backed Houthis as a fragile alliance between the two sides broke down.
Few local media reports have stated Houthi rebels had gained control of the majority of the country's capital from Saleh's forces.
There was no independent confirmation, but pictures circulated on social media appeared to show Mr Saleh's body.
Strongman Saleh had on Saturday bypassed his Houthi allies of three years, telling the Saudi-led military coalition in Yemen he was ready to negotiate if the crippling siege could be lifted.
But with Saleh's forces seemingly in disarray, it was not immediately clear if the Saudi-led coalition would be able to turn the split to its advantage.
It also shatters hopes by Yemen's Saudi-backed government that Saleh's recent split with the Iranian-backed rebels, known as Houthis, would have weakened them and given the government and the Saudi coalition backing a chance for a turning point in the stalemated war that has brought humanitarian disaster.
Saleh's vehicle was struck by an RPG fire on Monday and he was later shot to death, raising questions about what happens next in the almost three-year war that has killed at least 10 000 people. Witnesses said the bodies of slain civilians and fighters littered the streets as ambulances were unable to reach them.
Saleh's slaying likely gives the rebels the upper hand in the dayslong fighting for the country's capital, Sanaa.
According to the International Committee of the Red Cross (ICRC) on Tuesday, more than 230 people have been killed and around 400 injured in the Yemen war since the beginning of this month. It is reported that only five people attended the funeral.
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