Friday's bomb blast in Ashrafiya, a business centre full of banks, shops, universities and cafes, also injured 78 people.
Two of Lebanon's top anti-Syrian political leaders have accused Syrian President Bashar al-Assad of assassinating the Lebanese security official in the car bomb attack.
Mr Bowen has announced that despite the security concerns he will still make his first visit to Lebanon.
He is set to meet President General Michel Sleiman, Prime Minister Najib Mikati and other senior government officials and refugee organisations next week.
He will also visit Syrian refugee shelters in northern Lebanon, with the United Nations High Commissioner for Refugees.
"This will help to inform discussions about Australia's humanitarian program and consideration of ways we may be able to support Lebanon in the future," he said in a statement.
Mr Bowen's spokesman was tight-lipped about his itinerary, for security reasons.
The security official killed in the blast has been named as intelligence chief of Lebanon's Internal Security Forces, General Wissam al-Hassan.
NSW deputy police commissioner Nick Kaldas, who headed the 2009 UN investigation into the assassination of former Lebanese prime minister Rafik Hariri, worked closely with al-Hassan.
"It's an absolute tragedy ... he was a great family man," Mr Kaldas told ABC television on Saturday.
"His loss will be felt very deeply by the Lebanese community in Lebanon, the Middle East generally and the Lebanese community in Sydney."
He said al-Hassan had many relatives who were prominent members of the Lebanese community in Sydney.
