In testimony on Tuesday at his death penalty sentencing trial, Moussaoui was portrayed as a misfit who refused to follow orders.
The testimony of both was read to the jury, in one case because the witness is a captive whom the US government did not want to appear in court.
One operative, identified as Sayf al-Adl, a senior member of al-Qaida's military committee, stated that some time between 1 September 2001 and late July 2004, that Moussaoui, a French citizen, was "a confirmed jihadist but was absolutely not going to take part in the September 11, 2001, mission."
The September 11 Commission reported that the US had recovered from a safehouse in Pakistan a letter written by al-Adl describing the various candidates considered for the attacks.
The other - Waleed bin Attash, often known simply as Khallad - is considered the mastermind of the 2000 attack on the USS Cole and an early planner of the September 11, 2001 plot.
He said he knew of no part that Moussaoui was to have played in the September 11 attacks.
Khallad was captured in April 2003.
Their testimony backs up the claims of Khalid Shaikh Mohammed, chief organiser of the attacks.
He said in testimony read to the jury on Monday that Moussaoui had nothing to do with the plot but was to have been used for a second wave of attacks distinct from September 11.
Because Moussaoui has already pleaded guilty last April to conspiracy charges to hijack aeroplanes, the jury must only determine his sentence: death or life in prison.
Moussaoui says he was to fly a
fifth plane into the White House
To obtain the death penalty, prosecutors must prove that Moussaoui's actions resulted in at least one death on September 11.
Moussaoui said for the first time on Monday that he was supposed to pilot a fifth plane in the 9/11 plot and attack the White House.
He had previously denied a role in 9/11 and claimed to be part of a different plot.
The defence introduced an array of written testimony from these captives that was read to the jurors in an effort to undercut Moussaoui's dramatic testimony on Monday that he was to hijack a fifth plane on September 11 and fly it into the White House.
His lawyers were trying to undo damage he might have done to himself when he testified against their wishes.
Khallad portrayed Moussaoui as something of a loose cannon during a trip to Malaysia in 2000, where he met members of a radical group affiliated with al-Qaida.
Khallad said Moussaoui breached security measures and al-Qaida protocol.
For example, he called Khallad daily, despite instructions to call only in an emergency, to the point where Khallad turned his mobile phone off.
Another witness, Mustafa Ahmed al-Hawsawi, who served as a paymaster and facilitator for the September 11 operation from his post in Dubai, United Arab Emirates, said he had seen Moussaoui at an al-Qaida guesthouse in Kandahar, Afghanistan, in the first half of 2001, but was never introduced to him or conducted operations with him.
Moussaoui is accused of
breaching al-Qaida protocol
Al-Hawsawi said he provided money and tickets to four of the September 11 hijackers and to a fifth man, identified as Muhammed al-Qahtani, who was to be a hijacker but was denied entry to the United States before September 11 in Orlando, Florida.
In the written statement, Al-Hawsawi quoted Khalid Shaikh Mohammed as describing al-Qahtani as the last hijacker for the mission who would "complete the group".
Thus it appeared al-Qahtani was the so-called missing 20th hijacker of September 11, a role the government initially thought Moussaoui was to have played before his arrest a month earlier.
Also on Tuesday, Alan Yamamoto, the defence attorney, read a summary of three Federal Aviation Administration (FAA) intelligence reports on hijacking from the late 1990s and 2000, reports that concluded a hijacked airliner could be flown into a building or national landmark in the US.
However, this was "viewed as an option of last resort".
The FAA had reports of questionable reliability that Osama bin Laden had discussed hijackings and had discussed hijacking a US air carrier in an effort to free imprisoned Egyptian cleric Omar Abdel Rahman.
But the reports concluded that crashing a jetliner into a building appeared to be an unlikely option for the goal of winning Abdel Rahman's release because it offered no time to negotiate.