Pillay later denied having direct knowledge of their secret list of suspects, but her revealing remarks about the head of state were at odds with a policy of keeping the identity of alleged perpetrators under wraps pending any judicial process.
The UN investigators, who collect testimony in utmost secrecy and independently from Pillay, have previously said the evidence points to the highest levels of Syria's government, but have not named Assad or any other officials publicly. They have compiled secret lists of suspects and handed them to Pillay for safe storage, in hope that one day suspects will face trial for violations including torture and mass killings.
"They point to the fact that the evidence indicates responsibility at the highest level of government, including the head of state," Pillay told a news conference.
But Pillay said even she cannot unseal the confidential lists, and insisted she was only repeating what the investigators, led by Brazilian expert Paulo Pinheiro, had said.
Asked to clarify her remarks, she said: "I have not said that a head of state is a suspect. I was quoting the fact-finding mission, which said that based on their facts, responsibility points at the highest level."
World powers should make accountability for crimes committed in the civil war a priority ahead of Syrian peace talks set for January 22, she added.
The question of whether Assad can remain in power after the fighting stops has been one of the major areas of disagreement between the US and Russia, the two main sponsors of the peace talks.
Pillay and Pinheiro have repeatedly called for Syria to be referred to the International Criminal Court (ICC), a move that could lead to the prosecution of suspects.
Western countries that want Assad to step down should either stop dreaming or forget attending peace talks in January, the Syrian government said last Wednesday.
But former ICC judge Pillay said perpetrators of crimes must face justice. "Accountability should be key priority of international comm-unity, and I want to make this point again and again as the Geneva 2 talks begin," she said. "I reiterate my call to all member states to refer the situation to the ICC."
Both the Syrian government and opposition groups appear to be imposing sieges on contested areas as "a form of collective punishment", in violation of international humanitarian law, she said.
"Starvation as a method of warfare is prohibited," she said. "Now I mentioned some of these very serious factors, because as we look at the indictments before the ICC, these are some of the acts for which leaders have been indicted."
Pillay also condemned North Korea's detention of an 85-year-old American and said she was checking a report of recent mass executions in the country.
Merrill Edward Newman, a veteran of the Korean War, was detained on October 26 at the end of a tourist visit to North Korea, which is still technically at war with the US and South Korea.
Asked if North Korea, which is also known as Democratic People's Republic of Korea (DPRK), had acted legally by detaining somebody it regards as a prisoner of war, Pillay said she opposed its action.
She said: "I'm extremely shocked that this octogenarian has been forcibly held back in DPRK."