It was the latest in a string of awards the 1991 Nobel Peace Prize winner lost since Myanmar's military drove 720,000 Rohingya out of the Buddhist majority country in what the United Nations has called an act of genocide.
The London-based global human rights organisation said it was revoking the Ambassador of Conscience Award it gave Suu Kyi in 2009 while she was still under house arrest.
"Today, we are profoundly dismayed that you no longer represent a symbol of hope, courage, and the undying defence of human rights," Amnesty International chief Kumi Naidoo said in a letter to Suu Kyi released by the group.
"Amnesty International cannot justify your continued status as a recipient of the Ambassador of Conscience award and so with great sadness we are hereby withdrawing it from you."
Amnesty said it informed the 73-year-old of the decision last Sunday (Nov 11). She has so far issued no public response.
Suu Kyi was globally hailed as a freedom fighter who stood up to her country's feared military junta while spending 15 years under house arrest.
Her plight received added attention when she was visited by Hillary Clinton when the two-time US presidential candidate was still Secretary of State in 2011.
Suu Kyi then reaffirmed her commitment to working with the United States to bring democracy to her country of around 50 million people.
Her National League for Democracy (NLD) party swept to power in a 2015 landslide that brought hope of Myanmar correcting injustices inflicted over 50 years of brutal military rule.
But her tenure has been marred by a failure to speak up for Rohingya Muslims. Her government is also fighting an uphill struggle against corruption and local conflicts.
Amnesty said it believes thousands of Rohingyas were killed in Myanmar's western Rakhine province since the campaign began August 2017.
Many more are thought to have been either tortured or raped.
Myanmar has justified the military's actions as necessary to combat terrorism.
Amnesty conceded that the civilian government Suu Kyi informally heads does not directly control the powerful security services.
But it accused her of standing up for the crimes and "obstructing international investigations into abuses".
It added that human rights campaigners and journalists continued to be detained and intimidated by the government since her party's victory.
Suu Kyi was stripped of her honourary Canadian citizenship over her failure to speak up for the Rohingyas last month.
She has also lost numerous smaller awards from individual universities and local and regional governments.