The angry statement followed weeks of speculation on social networks of a split between the jihadist allies.
Al-Nusra "completely denies reports of a break-up with Al-Qaeda," the group said in a statement released on Twitter.
It said Al-Nusra "remains the backbone of jihadists" in Syria, "the first into battle, dedicated to unifying the ranks around sharia (Islamic law)... Righting injustice and defending the disadvantaged".
It denied "completely all reports of a meeting with Qatari or other intelligence services or seeking Qatari or Gulf funding, as this is contrary to the principles on which Al-Nusra has been based from the start".
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The idea of a rupture with Al-Qaeda emerged in early 2014 in Deir Ezzor when Al-Nusra militants allied with Islamic Front and the Free Syrian Army, "but it fizzled out", said Thomas Pierret, an expert at the University of Edinburgh.
"Al-Nusra's internal dynamics since the summer of 2014 do not point at all to a moderate tendency and a break with Al-Qaeda," he added.
Syria's conflict began in March 2011 as a popular revolt seeking democratic change, but later evolved into a full-blown civil war drawing jihadists fighting for Al-Nusra and the rival Islamic State group.