The footage was shot during the final stages of the Sri Lankan army's battle against Tamil Tiger separatists of the Liberation Tigers of Tamil Eelam (LTTE).
Alston said the authenticity of the video was established by three US-based independent, qualified experts he had commissioned to conduct an impartial evaluation after four Sri Lankan specialists had concluded that it was a fake.
He named the three as Daniel Spitz, a prominent forensic pathologist, Peter Diaczuk, a firearm evidence expert, and Jeff Spivack, a forensic video analyst.
"The independent experts' analyses also systematically rebutted most of the arguments relied upon by Sri Lanka's experts in support of their contention that the video was faked," Alston said.
"In light of these conclusions, I call for an independent inquiry to be established to carry out an impartial investigation into war crimes and other violations of international humanitarian and human rights law allegedly committed in Sri Lanka," he added.
Colombo should ask the United Nations to set up an independent commission of inquiry, he state.UN chief Ban Ki-moon said, through his spokesman Martin Nesirky, that "a full and impartial investigation into allegations of human rights (violations... in Sri Lanka) is critical if we are to confront impunity and bring the perpetrators of such violations to justice."
Nesirky said Ban informed Colombo that he was considering appointing a commission of experts "to advise him further and to assist the government in taking measures to address possible violations of human rights and international humanitarian law."
In its original report in August, Channel 4 had said that it could not verify the authenticity of the video which it received from a group called Journalists for Democracy in Sri Lanka.
The group claims the video footage was taken by a soldier using a mobile phone.
The disturbing footage shows a man dressed in army uniform shooting a naked, bound and blindfolded man in the back of the head, while the bodies of eight others can be seen nearby in a muddy field.
Alston said Spitz found the footage appeared authentic "especially with respect to the two individuals who are shown being shot in the head at close range."
And he added that Spivack's forensic video analysis "found no evidence of breaks in continuity in the video, no additional video layers and no evidence of image manipulation."
"While there are some unexplained elements in the video, there are strong indications of its authenticity," Alston said.
"In addition, most of the arguments relied upon by the government of Sri Lanka to impugn the video have been shown to be flawed."
When it was aired, the video was rejected by the Sri Lankan military as a fake aimed at discrediting the security forces.
Sri Lankan authorities have resisted international calls for a war crimes investigation after the United Nations alleged that more than 7,000 civilians had been killed during the first four months of 2009 alone.
The Tamil rebels were finally vanquished last May after nearly four decades of ethnic bloodshed that left between 80,000 and 100,000 people dead.
The government victory ended the LTTE's four-decade struggle for an independent Tamil homeland, one of Asia's longest-running ethnic conflicts.