Ali Hussein Alwan al-Azawi, nicknamed Abu Imad, suspected of being a top commander in al-Qaeda front organisation the Islamic State in Iraq, was captured in an operation in the capital, Baghdad military command spokesman Qassem Atta said.
"He is responsible for the explosion at the UN headquarters in Baghdad,'' Mr Atta said.
Before the US-led invasion of 2003, the suspect was a pilot for state-owned flagcarrier Iraqi Airways, he added.
The August 19, 2003 bombing which killed UN special representative Sergio Vieira de Mello and 21 of his colleagues marked the start of an escalating wave of attacks blamed on al-Qaeda and other insurgent groups.
The army spokesman said troops have also detained a Saudi national, Mohammed Abdallah Nasser, who's suspected of being an important al-Qaeda commander in Diyala province, north of the capital.
They are suspected of being behind a series of four bombings targeting the homes of policemen in the town which killed a total of seven people.