The transgender soldier had faced solitary confinement after being accused of having contraband items.
Manning, formerly known as Bradley, was convicted in 2013 of leaking thousands of secret files to Wikileaks.
She is currently serving 35-year sentence at a Kansas military prison.
The US Army declined to comment on the hearing, citing privacy laws, but earlier said such proceedings were a "common practice".
On her Twitter account, Manning said she would not be able to use the gym, library or go outdoors for three weeks as punishment.
Manning said the punishment also means she could spend longer in a high-security prison, as it represents a blot against her good behaviour records.
Among the banned items allegedly found in her cell was a tube of expired toothpaste, a copy of Vanity Fair magazine with transgender Caitlyn Jenner (formerly known as Bruce) on the cover and Malala Yousafzai's memoir.
Over 100,000 people signed a petition calling for the government not to sentence Manning to solitary confinement, the maximum penalty.
"When I spoke to Chelsea earlier today [Tuesday] she wanted to convey the message to supporters that she is so thankful for the thousands of people from around the world who let the government know that we are watching,'' her lawyer Chase Strangio said.
Manning, who legally changed her name in 2014, remains a soldier until her prison term ends.
Earlier this year, she was approved for hormone therapy after being diagnosed with gender dysphoria - the sense of one's gender being at odds with the sex assigned at birth.
Manning admitted handing more than 700,000 confidential documents to the anti-secrecy website Wikileaks while working as an intelligence analyst in Iraq.
US Army whistleblower Private Chelsea Manning has said she has been found guilty of violating prison rules and has been temporarily barred from recreational activities.