The sanctions against the two, whose names will be released tomorrow when the sanctions take effect, follow six months of fighting between troops loyal to President Salva Kiir and those behind his rival and former deputy Riek Machar.
More than 1.5 million people have been displaced and at least 10,000 people killed in the world's newest country amid what the EU said were "appalling human rights violations and crimes against humanity".
An existing arms embargo against South Sudan will remain in place, an official statement said.
The EU said it was "unacceptable" that a ceasefire agreement signed January 23 and reconfirmed May 9 continued to be breached.
"The EU has therefore decided to adopt as a first step restrictive measures against individuals responsible for obstructing the IGAD-led peace process, breaching the ceasefire and committing egregious human rights violations." the statement said.