It was also another successful night for England as Siobhan O'Connor and Fran Halsall secured gold in the 200m individual medley and 50m butterfly respectively, whilst hosts Scotland added three more medals.
Magnussen edged out fellow Australian Cameron McEvoy in a highly anticipated clash, although the winning time of 48:11sec didn't live up to expectations.
Tommaso D'Orsogna claimed bronze to make it an all-Australian podium.
McEvoy had surprisingly beaten Magnussen at the Australian trials in April and the man nicknamed "The Missile" said he planned to let his rival make the early pace before surging to victory in the final 25 metres.
"I had a race plan to let 'Cam' turn first and be ahead at 75m and really save myself for that last 25m to guarantee the win."
There was more gold and silver for Australia in the first event of the evening as Belinda Hocking held off teammate Emily Seebohm to win the women's 200m backstroke with Canada's Hilary Caldwell in third.
Ben Treffers and Mitch Larkin led home a third Aussie one-two of the evening in the men's 50m backstroke ahead of defending champion Liam Tancock of England in third.
O'Connor continued her stunning meet by adding gold in the 200m individual medley to her other three silver medals.
The 19-year-old smashed the Commonwealth Games record in a time of 2min 08:21 to beat reigning champion Alicia Coutts of Australia into second with Hannah Miley taking bronze for Scotland.
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