The hackers targeted a link-shortening service used by the Obama account, which is administered by the former campaign group Organizing for Action.
The resulting Obama tweet appeared to link to a Washington Post story about immigration.
But the link briefly carried users to a half-hour-long YouTube video that opens with footage of the 9/11 attacks.
The Syrian Electronic Army claimed credit for the attack in a statement obtained by the Associated Press. "Obama doesn't have any ethical issues with spying on the world, so we took it upon ourselves to return the favor," the statement said.
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