A surveillance camera in a Pentagon parking lot caught the moment that American Airlines Flight 77 slammed into the southwest side of the military headquarters.
Although the two video clips last about two minutes, the nose of the jet is seen for only a fraction of a second in one film before the explosion.
A huge ball of flame rises from the building and black smoke starts gushing out.
The attack, which came shortly after al-Qaeda hijackers flew two airliners into the World Trade Centre in New York, killed 189 people on the jet and inside the US defence department headquarters in the Washington suburbs.
The Pentagon on Tuesday handed the videos over to Judicial Watch, a watchdog group that sued for its release.
The lack of film evidence of the attack had fuelled conspiracy theories suggesting that the attack had been faked or engineered by the Pentagon against itself.
The justice department had previously blocked demands for their release on grounds that it was evidence in the prosecution of al-Qaeda plotter Zacarias Moussaoui.
But with Moussaoui convicted and sentenced to life in prison this month for his role in the September 11 conspiracy, the justice department agreed to release the videos, officials said.
Bryan Whitman, a Pentagon spokesman, said the videos appeared to show the same scene as a sequence of still images previously shown on US television tracking the airliners trajectory into the building.
"We fought hard to obtain this video because we felt that it was very important to complete the public record with respect to the terrorist attacks of September 11," said Tom Fitton, president of Judicial Watch.
"Finally, we hope that this video will put to rest the conspiracy theories involving American Airlines Flight 77," he said in a statement.
Judicial Watch has posted a copy of the video on its website at: http://www.judicialwatch.org/flight77.shtml
For a conspiracy theorist perspective, including elements of the new video, Pentagon Strike has a slick Flash presentation here: http://www.pentagonstrike.co.uk/flash.htm