Siddiqui faces up to life in prison when she is sentenced on May 6.
Her lawyers had tried to prove Siddiqui, who reported disturbing hallucinations involving her missing children, was insane. But a judge ruled her fit to stand trial.
Fauzia Siddiqui, her sister, told Al Jazeera the verdict had "rejuvenated" the family.
"And we're proud to be related to her," she said.
"America's justice system, the establishment, the war on terror, the fraud of the war on terror, all of those things have shown their own ugly faces."
Siddiqui, a neuroscientist who trained at the Massachusetts Institute of Technology in the US, was arrested by Afghan police in July 2008 in the town of Ghazni.
She had already caught the eye of human rights groups as prior to her arrest she had been missing for five years.
At the time of her arrest she was allegedly carrying containers of chemicals and notes referring to mass-casualty attacks and New York landmarks, leading some in the US press to dub her "Lady Qaeda".
But Siddiqui was not charged in connection with those materials and the charges she was convicted of do not mention terrorism.
Instead, the charges against her centred on an incident the next day in the Afghan police compound, where US soldiers and FBI agents sought to question her.
Siddiqui grabbed a US warrant officer's rifle while she was detained for questioning in July 2008 in Afghanistan's Ghazni province and fired at the FBI agents and military personnel, who returned fire.
None of the US agents or personnel were injured but Siddiqui was shot in the incident.
"She saw her chance to kill Americans and she took it," Christopher LaVigne, the prosecutor, told jurors.
But Linda Moreno, Siddiqui's defence lawyer, said during the trial that there was no evidence the rifle had ever been fired, since no bullets, shell casings or bullet debris were recovered and no bullet holes detected.
Moreno also said the testimony of the government's six eyewitnesses contradicted one another on Siddiqui's location in the 28sq m room, the number of bullets fired and who was present.
|Siddiqui shouted that the verdict was "from Israel" as the jury was leaving court [AFP]
Tina Foster, a spokeswoman for the Siddiqui family and the executive director of the International Justice Network, told Al Jazeera that there were "a lot of unfair rulings made by the judge and I think we can expect to see an appeal".
"Aafia walked into that courtroom already labelled a terrorist by prosecutors, despite the fact that she was not on trial for any terrorism related offence," Foster said.
"I think that if there was credible evidence that Aafia Siddiqui had been involved in any sort of terrorist activities ... any sort of plot against the United States that she had been involved in, we would have seen prosecutions for those crimes," she said.
"One has to wonder whether the reasons she was in custody to begin with are ever going to be addressed by the government of the United States.
"Why she had been on that wanted list, and why all of these allegations that were not made in court have continued to be leaked to the media and have continued to paint Dr Aafia in a negative light despite the fact that she has never been charged with any terrorism activity."
Pakistan's embassy in Washington also voiced its criticism, saying it was "dismayed over the unexpected verdict".
"The government of Pakistan made intense diplomatic and legal efforts on her behalf and will consult the family of Dr Aafia Siddiqui and the team of defence lawyers to determine the future course of action," it said.