Speculation about the assassination of Younes ranged widely. There were reports that he had been suspected of feeding the Gaddafi camp with information. One rebel commander said Islamists whom Younes had targeted in his job as interior minister may have been to blame.
The United States, which like some 30 other nations has formally recognised the opposition, said Younes's death was a blow but called for solidarity among the rebels.
"What's important is that they work both diligently and transparently to ensure the unity of the Libyan opposition," State Department spokesman Mark Toner said in Washington.
On Friday, weeping relatives and supporters brought Younes's coffin into the main square of Benghazi to mourn him, as fighters fired guns in the air.
Some family members vowed allegiance to the rebels' political leader. "A message to Mustafa Abdel Jalil: We will walk with you all the way," nephew Mohammed Younes told hundreds of mourners in the main square.
RUMOURS OF SECRET TALKS
Younes, from eastern Libya where the rebels are strongest, had been Gaddafi's interior minister but switched sides to become the military chief in the rebel Transitional National Council.
Rebel defence minister Omar Hariri, visiting the west, said Younes's death would have an impact on rebel fighters. "But they will recover, and there will be other leaders," he said.
Rebels took swathes of Libya soon after launching their uprising in February against Gaddafi's 41 years of domination of the oil-producing North African state, but have made few recent advances despite the support of NATO air strikes.
They said they had seized several towns in the Western Mountains on Thursday but are yet to make a major breakthrough.
A rebel commander near Ghezaia told Reuters on Friday that around 100 insurgents had taken control of the town, from which Gaddafi forces had dominated plains below the mountains.
Reuters could not go there to confirm the report as rebels said the area could be mined. But through binoculars from a rebel-held ridge near Nalut, reporters could see no sign of Gaddafi's forces in Ghezaia.
Fighters on the front line near the town of Misrata said they viewed Younes as a martyr and would avenge his death.
"It will be an extra motive for us in the fight against the tyrant," said Khaled al-Uwayyib.
With prospects fading for a negotiated settlement, the five-month-old civil war will grind on into the Muslim holy month of Ramadan in August.
Nick Witney, analyst at the European Council on Foreign Relations in Paris, said the West had hoped for a "nice simple conflict" with right prevailing, but this had ignored the nuanced, tribal nature of Libyan politics.
"It was a brave and right thing to do," he said. "But I feel we've lost the moral high ground a bit and wandered into something that will be prolonged and messy, but we're not in a position to sort out."
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