In a keynote address at a conference on democracy in the Arab world, Ban Ki-moon said the days of one-man rule and family dynasties are over in the Middle East.
"Today, I say again to President (Bashar) Assad of Syria: Stop the violence. Stop killing your people," Ban said.
Assad is trying to crush a 10-month-old uprising that he blames on terrorists and armed gangs. The UN estimates more than 5,000 people have been killed in the government's crackdown.
Thousands of people have been killed in the Syrian government's crackdown on a 10-month-old uprising, which has turned increasingly violent in recent months. The Syrian regime blames the revolt on terrorists and armed gangs, rather than protesters seeking an end to nearly four decades of Assad family rule.
Syria's state news agency meanwhile said Assad granted a general amnesty for crimes committed during the unrest of the past 10 months.
Arab League observers began work in Syria on December 27 to verify whether the government is abiding by its agreement to end the military crackdown on dissent and release prisoners, but the bloodshed has only increased. The UN says about 400 people have been killed in the last three weeks alone, on top of an earlier estimate of more than 5,000 killed since March.
Opposition and army defectors meanwhile have increasingly been taking up arms to fight back against government forces, raising concerns of civil war in the predominantly Sunni country, ruled by Assad's minority Alawite sect.
"It is sometimes said that authoritarian regimes, whatever else their faults, at least kept a lid on sectarian conflict. This is a cruel canard," Ban said. "Yet it would be equally mistaken to assume that all of the new regimes now emerging will automatically uphold universal human rights," he added.
Ban acknowledged challenges facing Arab states in the wake of the uprisings sweeping the Arab world, in Tunisia, Egypt, Libya and Syria.
"Democracy is not easy," he said. "It takes time and effort to build. It does not come into being with one or two elections. Yet there is no going back."
He encouraged Arab countries to usher in real reforms and dialogue, and to respect the role of women and the young.
"The old way, the old order, is crumbling," Ban said. "One-man rule and the perpetuation of family dynasties, monopolies of wealth and power, the silencing of the media, the deprivation of fundamental freedoms that are the birthright of every man, woman and child on this planet - to all of this, the people say: Enough!"
The UN chief also urged an end to "Israeli occupation of Arab and Palestinian territories ... Settlements, new and old, are illegal. They work against the emergence of a viable Palestinian state."
The leader of Qatar was yesterday quoted as saying that Arab troops should be sent to Syria to stop a deadly crackdown on anti-government protests.
Sheik Hamad bin Khalifa Al Thani's comments to CBS' "60 Minutes," which will be aired today, are the first statements by an Arab leader calling for the deployment of troops inside Syria.
Asked whether he is in favour of Arab nations intervening in Syria, Sheik Hamad said, "For such a situation to stop the killing some troops should go to stop the killing."
Qatar, which once had close relations with Damascus, has been a harsh critic of the crackdown by Assad's regime. The wealthy and influential Gulf state withdrew its ambassador to Syria in the summer to protest the killings.
Since the Arab Spring began more than a year ago, Qatar has taken an aggressive role, raising its influence in the region. It contributed war planes to the Nato air campaign in Libya, tried to negotiate an exit for Yemen's protest-battered president Ali Abdullah Saleh, and has taken the lead in Arab countries pressuring Assad.
It was not clear how many prisoners would be affected by today's pardon issued by Assad.
SANA said the amnesty covers those who have peacefully demonstrated, those who have carried unlicensed weapons and those who handed over their weapons to authorities before the end of January. It also applies to army deserters who fled military service if they turn themselves in before January 31.
Since the outbreak of the uprising against Assad's rule in March, Assad has freed 3,952 prisoners, according to SANA.
The opposition claims there are thousands more in Syrian prisons.
