The verdict by the eight-member panel came after about three hours of deliberations in a top security court house in Rome.
The nine were arrested in February 2002, on suspicions they were planning to poison the embassy's water supply with a mildly poisonous chemical compound found at the Rome apartment where four of the suspects were living.
Maps indicating the US embassy were found outside the same apartment.
They were charged with association aimed at international terrorism - a charge introduced after the September 11 attacks as part of Italy's efforts to crack down on suspected terrorists.
"It's a huge satisfaction," Fabio Frattini, a lawyer for two of the Moroccans, said soon after the verdict was handed down.
"It's been shown that these people had no link to international terrorism."
Prosecutor Franco Ionta had asked the court to convict four of the defendants, seeking a prison term of up to seven years and six months. He had asked the court to acquit the remaining five, citing lack of evidence.
"We have been left without work and without homes, and in the end we get acquitted"
But the defendants denied any wrongdoing, arguing the case was the fruit of misunderstanding and was fed by general fear of international terrorist groups striking in Europe.
Defence lawyers have pointed out that the suspects were released from arrest in September on grounds that they posed no threat to public safety.
"Basically, justice has been done," said Said Iqbal, one of the Moroccans who Ionta had asked the court to acquit.
However, Iqbal noted that he and the other suspects had been detained for one and half years years following their arrests. "We have been left without work and without homes, and in the end we get acquitted," he said.
In a separate case, the court also acquitted a Pakistani, a Tunisian and an Algerian, who were accused of forming a terrorist cell based around a Rome mosque, and also arrested in early 2002.
The three were accused of association aimed at international terrorism, based on phone taps in which police allege that they heard the suspects talking about arms, including bombs and Kalashnikovs.
Prosecutors had sought up to eight years and four months in prison.
"What we have been saying all along has been confirmed - that there was not any element of proof in this case," said Simonetta Crisci, defence lawyer for Ahmad Nasir, the Pakistani who prosecutors had said was the ringleader of the cell.
"Let's ask ourselves why there was a terror campaign by police and magistrates here in Italy after 11 September," Crisci said.