In a report, the UK-based human rights group says the abuse has been taking place during a disarmament campaign in the eastern Jonglei state.
Amnesty urges South Sudan to take "immediate action" to end the violence.
The government in Juba has played down the scale of the violations, saying they are isolated cases.
Amnesty says its researches interviewed scores of people in the region, who described widespread torture and abuse against civilians, including children as young as 18 months old.
It also says that in some cases the security forces looted property and destroyed crops.
"Far from bringing security to the region, the SPLA (South Sudan Army) and the police auxiliary forces have committed shocking human rights violations," said Audrey Gaughran, Amnesty's Africa director.
He accused the authorities of "doing very little to stop the abuse".
The government launched Operation Restore Peace in March in response to ethnic clashes in Jonglei in which hundreds of people were killed.
South Sudan - which gained independence just over a year ago - has previously sought to play down the accusations, the BBC's Grant Ferret says.
The danger, though, is that the alleged abuse could fuel resentment and a new round of conflict, our correspondent adds.
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