"The conflict must stop now," he added.
Soon after Putin's announcement, explosions were heard in the Ukrainian capital Kyiv and other cities.
Weeks of intense diplomacy at the UN and elsewhere to avert war and the imposition of Western sanctions on Russia failed to deter Putin, who had massed between 150,000 and 200,000 troops along the borders of Ukraine.
The United States said it would present a resolution condemning Russia's aggression at the Security Council on Thursday, with a vote expected the following day.
"The council will need to act," said US ambassador Linda Thomas-Greenfield.
Wednesday's emergency session involved some particularly heated exchanges between the Ukrainian and Russian envoys.
"There is no purgatory for war criminals. They go straight to hell, Ambassador," Ukraine's Sergiy Kyslytsya told his Russian counterpart Vassily Nebenzia.
Nebenzia replied that Moscow's aggression was not aimed at the Ukrainian people, but rather "the junta that is in power in Kyiv."
Speaking to reporters after the session, Guterres said a full-scale war would come at enormous human cost and have a devastating economic impact that would be felt around the world.
"What is clear for me is that this war doesn't make any sense... And it will cause, if it doesn't stop, a level of suffering Europe has not known since, at least, the Balkan crisis," he added.
Warnings of a possible Russian invasion had mounted over weeks, as Moscow massed troops on Ukraine's borders and earlier this week recognized the independence of two breakaway eastern Ukraine regions.
Putin has defied a barrage of international criticism over the crisis, with some Western leaders saying he was no longer rational.
His announcement of military action came after the Kremlin said rebel leaders in eastern Ukraine had asked Moscow for military help against Kyiv, and ahead of a last-ditch summit involving European Union leaders in Brussels planned for Thursday.