The 15-member body on Thursday called on Lebanon to extend control over the entire country by deploying its army in all areas and "to put an end to all attacks emanating from its territory".
The Security Council last September demanded foreign forces withdraw from Lebanon and militias, such as Hizb Allah, be disarmed.
"In this context, they expressed serious concerns at (Wednesday's) attack," the council said in a press statement.
On Thursday, Israeli helicopters struck at Hizb Allah a day after the fighters killed an Israeli officer in the worst border violence in six months.
Israeli aircraft fired missiles at Hizb Allah positions and later raked hillsides with machine-gun fire inside South Lebanon, witnesses said.
Anne Patterson, the acting US ambassador, criticised the statement for not specifically mentioning the September Resolution 1559 and for not saying that Hizb Allah started the
Other members said the council statements had not blamed Israel in previous incidents when it fired the first shot.
Israeli aircraft fired missiles at
Hizb Allah positions
"This was a difficult negotiation," Patterson said. "The statement was weaker than we would have liked."
"It did not recognise the fault of Hizb Allah in attacking," she said. "The Lebanese armed forces need to deploy into southern Lebanon as quickly as possible and take control of their own territory."
Hizb Allah was instrumental in ending Israel's 22-year occupation of southern Lebanon in 2000. The two foes have clashed sporadically in the Shebaa Farms area since then.
Lebanon and Syria say Shebaa Farms is Lebanese territory, but UN cartographers who surveyed the border after the Israeli withdrawal determined it was part of the Syrian Golan Heights that Israel has occupied since the 1967 Arab-Israeli war.
The UN has said the two nations were free to demarcate their own border, which they have not done.
The US called for a UN briefing on the clash after Israel's UN Ambassador Dan Gillerman filed a protest with the Security Council and Secretary-General Kofi Annan.
Gillerman said: "The message from the Security Council today was a very strong one. This is an act of terrorism taken across the border ... by a militia that is active within a sovereign country."