"There are no words to express… this tragedy," Antonio Guterres, the United Nations high commissioner for refugees, told reporters in Geneva on Tuesday.
The exodus shows no sign of abating and risked destabilising the region, Guterres said.
He said the two-million milestone — a ninefold increase in 12 months — was not just an appalling statistic, but represents two million individual stories.
"Two million people, many have lost their houses, members of their families, their possessions."
On average, some 5,000 Syrians flee their country every day, the UNHCR said.
Guterres said the majority of the refugees head to Lebanon and other neighbouring countries where concern is mounting of a spillover of the Syria conflict.
The flow of refugees has gathered momentum in recent weeks amid fears of Western military action against the Syrian regime over its alleged use of chemical weapons against civilians.
Guterres said with the number of displaced continuing to escalate, the Syria refugee crisis today is without parallel worldwide.
"At this particular moment it's the highest number of displaced people anywhere in the world," he said.
"Syria has become the great tragedy of this century, a disgraceful humanitarian calamity with suffering and displacement unparallelled in recent history."