Syria authorities target children, says UN rights chief
Ms Pillay said President Bashar al-Assad could end the detentions and stop the killing of civilians immediately, simply by issuing an order.
Syria has accepted a peace plan, amid scepticism about its intentions.
The peace plan was put forward by UN and Arab League envoy Kofi Annan.
Navi Pillay told the BBC that the Syrian leader would face justice for the abuses carried out by his security forces.
Asked if President Assad bore command responsibility for the abuses, she said: "That is the legal situation. Factually there is enough evidence pointing to the fact that many of these acts are committed by the security forces [and] must have received the approval or the complicity at the highest level.
"Because President Assad could simply issue an order to stop the killings and the killings would stop."
Ms Pillay said she believed that the UN Security Council had enough reliable information to warrant referring Syria to the International Criminal Court (ICC).
AnalysisNavi Pillay is one of the most experienced international war-crimes experts.
Before taking up her UN role as high commissioner for human rights, she served as a judge on the International Criminal Court (ICC) and the tribunal investigating the Rwandan genocide.
As a lawyer of more than 45 years experience Mrs Pillay has learned to choose her words carefully. That is why her forthright comments on President Bashar al-Assad will arouse interest.
"They've gone for the children - for whatever purposes - in large numbers. Hundreds detained and tortured... it's just horrendous.
"Children shot in the knees, held together with adults in really inhumane conditions, denied medical treatment for their injuries, either held as hostages or as sources of information."
Ms Pillay said anyone who committed such violations would be held to account.
"There is no statute of limitations so people like [Mr Assad] can go on for a very long time but one day they will have to face justice."
Opposition meets The UN says more than 9,000 people have been killed since the uprising against President Assad began a year ago.
Late on Tuesday, several Syrian dissident groups meeting in Istanbul agreed to recognise the Syrian National Council as the official representative of the Syrian people.
The BBC's Jonathan Head at the gathering said none of the delegates he spoke to believed President Assad was sincere, and the Syrian opposition would never accept any deal allowing him to remain in power.
But our correspondent says their disunity was openly on display, with constant disputes and walkouts.
Earlier, a spokesman for Kofi Annan said he considered the Syrian acceptance of the six-point peace plan an "important initial step" but that implementation was key.
Mr Annan - currently in Beijing for talks with Chinese Premier Wen Jiabao - has written to President Assad urging him to put his commitments into immediate effect.
US Secretary of State Hillary Clinton said President Assad would be judged by events.
"Given Assad's history of over-promising and under-delivering, that commitment must now be matched by immediate actions," she said.
Annan's six-point peace plan1. Syrian-led political process to address the aspirations and concerns of the Syrian people
2. UN-supervised cessation of armed violence in all its forms by all parties to protect civilians
3. All parties to ensure provision of humanitarian assistance to all areas affected by the fighting, and implement a daily two-hour humanitarian pause
4. Authorities to intensify the pace and scale of release of arbitrarily detained persons
5. Authorities to ensure freedom of movement throughout the country for journalists
6. Authorities to respect freedom of association and the right to demonstrate peacefully
However, it does not impose any deadline for Mr Assad, or call for him to leave power.
The BBC's Barbara Plett at the UN says that, despite the scepticism, this is a new situation because it is the first strategy for ending the conflict that has the backing of the entire Security Council, including Syria's allies Russia and China.
She says it seems it was this international unity which forced President Assad to accept the plan.
Mr Annan has written to Mr Assad urging him to put his commitments into immediate effect.
BBC Middle East editor Jeremy Bowen says the agreement is not as strongly worded as earlier UN resolutions, but it can be regarded as more pressure on Mr Assad and his government, which he seems to have decided that he cannot ignore.
However, implementing the plan is another matter, our correspondent adds.