Magnussen edged out compatriots Cameron McEvoy and Tommaso D'Orsogna with an impressive swim of 48.11 seconds.
Australians claimed 10 medals in a one-sided session that landed them four golds, four silvers and two bronze medals to take their haul so far to a table-topping 38.
The 23-year-old Magnussen, who won a silver and bronze at the London 2012 Olympics, now has two Glasgow golds, having won the 4x100m freestyle relay on Friday.
"For me, it was a two-man race," Magnussen told reporters.
"The plan was to sit next to Cam (McEvoy) and switch it up when I needed to. I felt like I took a lot of pressure off myself and I was able to enjoy it."
It was the first time that an Australian has won the event since five-times Olympic champion Ian Thorpe in 2002 in Manchester. The country have now won this race nine of the 12 times it has been contested at the Games.
The Aussie gold rush started with Belinda Hocking storming to victory in the 200m backstroke in a Games record 2:07.24.
"It feels awesome. I am really happy. I was so nervous but I had some confidence from last night (she won bronze in the women's 100m backstroke)," Hocking said.
Even when an Australian could not win they ensured there was still green and gold on the podium.
Alicia Coutts snatched silver from home favourite Hannah Miley as they were left in the wake of England's Siobhan O'Connor who swam a Games record in the 200m individual medley.
Ben Treffers and Mitch Larkin secured an Australian one-two in the 50m backstroke with England's Liam Tancock third.
England's Fran Halsall defended her 50m butterfly title with a new Games and British record of 25:20.
The evening's action concluded with an emphatic Australian performance to win a thrilling 4x200m freestyle relay, edging out Scotland and South Africa..
(Reporting by Sam Holden; editing by martyn herman)
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