In a documentary to coincide with the anniversary, "there will be the first direct confession as to how al-Qaeda planned and executed 11 September," documentary maker Yosri Fouda told Reuters news agency.
The first part of the documentary was aired on Thursday and the second part, which is said to show the confessions, will be shown next week.
Al-Jazeera, based in the Gulf state of Qatar, caught the world's attention when it began airing statements from al-Qaeda leader Osama Bin Laden soon after the attacks last year.
However the Bush administration complained the channel gave Bin Laden and his aides a forum to address the Arab public.
Anniversary programmes
An official from the television station identified the two alleged al-Qaeda members as Ramzi Bin al-Shaibah and Khaled al-Sheikh Mohammad.
A spokesman for the channel claimed that the two men shared a flat with Mohamed Atta, one of the 19 hijackers who the US says were involved in the 11 September attacks.
According to Reuters, the interviews took place in Karachi, Pakistan, and were arranged by a liaison officer from al-Qaeda, whom the channel identified as Abu Bakr.
Al-Jazeera is marking the 11 September anniversary by showing interviews with al-Qaeda chiefs and programmes on the long-term impact of the attacks.
"We have two types of programmes to mark the anniversary - human reports on how the attacks and the war affected the lives of the American and Afghan people, and investigative reports on the attacks themselves," Ibrahim Helal, chief editor of al-Jazeera, told the Associated Press news agency.
A promotional video of the two-part documentary shows one of the planes slamming into the first tower, Osama Bin Laden speaking briefly and a Muslim cleric reading from the Koran.
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