A surveillance camera in a Pentagon parking lot caught the moment that American Airlines Flight 77 slammed into the south west side of the military headquarters in the US capital Washington DC and burst into a ball of flames.
The nose of the jet is seen for only a flash before the explosion.
The two video clips run for about two minutes, and depict black smoke gushing out from the building.
The attack set off fires in part of the building and killed 125 people inside, along with 59 passengers and crew on board the aircraft.
The release of the video comes in response to a Freedom of Information Act request by legal watchdog group Judicial Watch.
The group said it hopes the release will dispel conspiracy theories about the Pentagon crash that circulated, fuelled by the lack of film evidence of the attack.
Some theories suggested that the attack had been faked or engineered by the Pentagon against itself, and others claimed the aircraft was struck down by a missile or shot down in flight.
"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 Judicial Watch president Tom Fitton.
"Finally, we hope that this video will put to rest the conspiracy theories involving American Airlines Flight 77," he said in a statement.
The group said it would post a copy of the video on its website, www.judicialwatch.org.
The Pentagon admitted having the video last year, but it said it could not release it at the time because it was part of its investigation into Zacarius Moussaoui, Judicial Watch said.
But with Moussaoui convicted and sentenced to life in prison earlier this month for his role in the September 11 conspiracy, the Justice Department agreed to the videos release, officials said.
A Pentagon spokesman, Bryan Whitman, 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.
Two tapes were released from different security cameras show the building from different angles.
Still photographs from the video have previously been leaked.
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 Defence Department headquarters in the Washington suburbs.
Moussaoui was convicted and sentenced to life in prison earlier this month for his role in the September 11 conspiracy, prompting the Justice Department to agree to releasing the footage.