Barak was addressing the House as part of the government rebuttal to a no-confidence motion presented for a vote by Kadima, Meretz, and the Arab parties.
The no-confidence motion was denied by a majority vote.
"This was not the result we were after and we are dealing with it. We will continue to deal with it to ensure security, to prevent Hamas from gaining power in Gaza, for the negotiations to free Gilad Shalit and to ensure we thwart Gaza terror," said Barak.
"Redirecting the Rachel Corrie to Ashdod and targeting the five terrorists today, were both done by the same Naval Commando, by the same IDF, the same soldiers and the same commanders.
"They are living proof that the pride that so many of us feel towards our soldiers, the anger we feel towards the flotilla organizers and the frustration we feel with the results – are all understandable, justified and human."
Barak went on to question the timing and validity of the no-confidence motion, and praised the government's handling of the events, saying that "discretion and cool are needed no only under uncertain conditions and threats, but also while facing the challenges of exhausting any and all diplomatic avenues."
Barak dismissed calls to lift the Gaza blockade: "My answer to this in unequivocal – the blockage and the monitoring of maritime cargo headed to Gaza is necessary to prevent delivery of rockets, missiles, arms and munitions.
"There are 1.5 million people in Gaza. Only one truly needs humanitarian aid. Only one of them is locked away, deprived the light of day and human company," he said, referring to captive IDF soldier Gilad Shalit.
Barak was repeatedly interrupted by various Knesset members, despite Knesset Speaker Reuven Rivlin request that all House members exercise restraint.
'Kahane week in the Knesset'
Prior to Barak, MK Ahmad Tibi (United Arab List-Ta'al) took the podium, and chose to address mainly the hostility encountered by Arab MKs since the raid.
"This week can be called 'Kahane week.' Some rightist MKs challenge us, but this Knesset has MKs unworthy of the term, ones who are practically an embarrassment and make you feel not only contempt, they make you not even want to look at them.
"How embarrassing that Israel, which presents itself as a democracy, cannot bear to hear a (contradictory) opinion. It reverts to a narrow, nationalistic bubble that says 'we are the majority and we will trample,' especially when it comes to Arab MKs."
Surprisingly, Zuabi's speech before the house encountered only a minimal response. After her last speech, given just after the flotilla raid, sparked one of the most boisterous sessions the House has even known, Monday's speech, which focused on the blockade, was marked with only a few interjections.