The decision means the trial will now move into a second phase, beginning on Thursday, to determine whether Moussaoui deserves the death penalty.
Survivors of the September 11, 2001, attacks and families of victims will testify in this second phase.
Moussaoui, who has made frequent outbursts during the hearings, was defiant as he was led away from court following the jury's decision.
"You will never get my blood, God curse you all," he shouted at jurors.
Summing up the verdict Judge Leonie Brinkema declared the jury had found against Moussaoui on three capital counts of conspiracy to commit terrorism, conspiracy to use weapons of mass destruction and conspiracy to destroy aircraft.
During its deliberations, the jury has asked only one question, seeking a definition of "weapon of mass destruction."
One of the three convictions for which Moussaoui, a French citizen, could be executed is conspiracy to use weapons of mass destruction.
The jurors were told that a plane used as a missile - the tactic employed on September 11 - qualifies as a weapon of mass destruction.
Moussaoui pleaded guilty last April to conspiring with al-Qaeda to hijack aircraft and other crimes.
At the time, he denied being part of the 9/11 plot, saying he was being trained for a separate attack, but he changed his story when he took the stand and claimed he was to have flown a hijacked airliner into the White House that day.
The jury must find that Moussaoui was responsible for at least one death on September 11, for him to be eligible for execution.
Moussaoui was in jail at the time of the attacks, but prosecutors argue federal agents would have been able to thwart or at least minimise the attacks if he had revealed his al-Qaida membership and his terrorist plans when he was arrested and interrogated by federal agents.
The US government, which saw its failure to stop the attacks exposed in a catalogue of bungles, missteps and mistakes highlighted by defense lawyers, welcomed a legal victory in the war on terror.
"We are pleased with the jury's ruling in this important case," Justice Department spokeswoman Tasia Scolinos said in a statement.
"Our efforts on behalf of the victims of 9/11 will continue as we pursue the next phase of this trial."
However, a French lawyer representing Moussaoui said defence lawyers would wage an "at all costs" battle to save his life.
"We are going to do all we can in an attempt to convince the jury ... that the death penalty should not be carried out," Francois Roux told AFP in a telephone interview.
Moussaoui's defence team had urged the jury not to make the 37-year-old Frenchman a hero, and to deny him the martyrdom on which he appeared to have set his sights.