Israel had maintained official silence over Wednesday's raid, which Syria said targeted a military research centre north-west of Damascus.
"I cannot add anything to what you have read in the newspapers about what happened in Syria several days ago," Mr Barak told a security conference in Munich.
"But I keep saying frankly that we said – and that is another proof that when we say something we mean it – we say that we don't think it should be allowable to bring advanced weapons systems into Lebanon."
Diplomats, Syrian rebels and security sources said Israeli jets bombed a convoy near the Lebanese border on Wednesday, apparently hitting weapons destined for the Lebanese militant group Hezbollah, which fought a 34-day war with Israel in 2006.
Syria denied the assertions, saying the target was the Jamraya complex on the north-western fringes of Damascus.
Some of the diplomats and security sources said the apparently contradictory accounts might refer to the same incident, given Jamraya's proximity to the border and the fact that vehicles inside the complex were hit as well as buildings.
Syrian television broadcast footage from the Jamraya base for the first time, showing extensive damage to buildings and several heavy military vehicles that appeared capable of carrying missiles. At least one vehicle, with light desert khaki markings, was equipped with what looked like a satellite dish.
Several burnt-out cars and lorries could also be seen in the footage, as well as the badly damaged interior of an office.
Until Mr Barak's comment, Israel had maintained silence over the attack, as it did in 2007 when it bombed a suspected Syrian nuclear site – an attack that passed without Syrian military retaliation.
Syria's ambassador to Lebanon warned on Thursday that his country could take "a surprise decision to respond", but gave no details. Damascus protested to the United Nations, saying it considered the raid a violation of a 1974 military disengagement agreement that followed the last major Israeli-Syrian war.
In his first reported response to the attack, President Bashar al-Assad yesterday accused Israel of seeking to destabilise Syria and said Damascus was able to confront "current threats ... and aggression" against it.
Mr Assad made the remarks in a meeting with Saeed Jalili, Iran's national security council secretary, who pledged Tehran's "full support for the Syrian people ... facing the Zionist aggression, and its continued coordination to confront the conspiracies and foreign projects".
The Syrian president, Shi'ite Iran's closest Arab ally, is battling a 22-month uprising in which 60,000 people have been killed. Mr Assad says the rebels are Islamist terrorists funded and armed by Turkey and Sunni Muslim Gulf Arab states.
Meanwhile, a former member of the Syrian parliament and three members of his family have been killed in a rebel-held area near the northern city of Aleppo.
Ibrahim Azzouz's car came under fire near the city's airport, killing him along with his wife and two daughters.