The two men, one from government forces and one from the rebels, were "responsible for perpetrating unthinkable violence against civilians," US Secretary of State John Kerry told reporters.
The move comes against Marial Chinoum, a commander of the South Sudanese presidential forces, and Peter Gadet, a leader of the anti-government forces, and only days after Kerry visited Juba.
"We will do our utmost to prevent South Sudan from plunging back towards violence and despair," Kerry said after meeting EU foreign policy chief Catherine Ashton in Washington.
The sanctions move will be a bitter-sweet one for Kerry because Washington was the prime mover enabling South Sudan to split from Sudan to become independence in 2011.
UN chief Ban Ki-moon visited Juba today as rebels and government forces battled for control of a key oil town, in the latest major drive for a ceasefire in a war that has seen the nation collapse amid a brutal cycle of war crimes.
Ban said South Sudan rebel chief Riek Machar had promised to attend fresh peace talks tentatively scheduled to take place on Friday in Ethiopia.