Moussaoui, 37, has admitted guilt, and a jury in Virginia is hearing submissions to decide whether to sentence him to death.
Prosecutor David Raskin quoted flight attendant Amy Sweeney from a phone call to the ground minutes before her flight slammed into New York’s World Trade Centre, as saying: “Oh my God, we are way too low.”
He continued to read accounts of the highjackings, as relatives watched the proceedings on televisions in courtrooms around the country.
Defence lawyers retaliated by criticising US government claims that Moussaoui knew Al-Qaeda planned to use hijacked airliners as missiles.
Prosecutors argue that by saying nothing, Moussaoui shares the guilt for nearly 3,000 deaths on September 11, even though he was in jail at the time.
The defence also drew an admission from an FBI investigator that no evidence has been found to show that the defendant had contacted the 19 hijackers.
Prosecutors also returned a separate FBI special agent, Michael Anticev, to the witness box.
He read a passage from a captured al-Qaeda terrorism manual saying that operatives were trained to lie if captured to shield co-conspirators and allow planned attacks to go ahead.
“I don’t think anybody was looking into people using planes as weapons, as opposed to the more traditional hijacking,” Mr Anticev said during his testimony.
Moussaoui’s court-appointed lawyers, who he has rejected, are painting him as a lone bumbler who was not included by the real terrorists involved in the September 11 attacks.
The 37-year-old Frenchman of Moroccan heritage is the only man so far tried in a US courtroom in connection with the September 11 strikes in 2001.
Jurors are to decide whether he caused the death of anyone on September 11, and is therefore eligible to be executed by lethal injection.
In the courtroom on Tuesday, Moussaoui’s mother sat three rows behind her son in the public gallery, sobbing quietly, as her son sat silently.
She later claimed her son’s calm behaviour, at odds with furious outbursts during jury selection last month, show he has been drugged.