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.
"Obviously it wasn't the quickest time I've done in recent times, but I wasn't really focused on times tonight," said Magnussen.
"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,” he added.
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.
Australia made it four golds from four in the relays as the men's 4x200m freestyle team held off an impressive challenge by Scotland and South Africa, who finished in second and third respectively.
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

"I'm absolutely over the moon. I knew it would be so hard to get a medal because of the strength of the field so I can't ask for any more," said O'Connor.
And Halsall added her second gold in as many days with another Commonwealth Games record of her own in a time of 25:20sec in the 50m butterfly.
Arianna Vanderpool Wallace won Bahamas' first medal of the Games with silver whilst Brittany Elmslie added to Australia's medal haul with bronze.
New Zealand claimed their first gold of the Games in the pool through Sophie Pascoe as she won the women's para-sport 100m breaststroke SB9.
Australia's Madeleine Scott claimed silver and there was another bronze for the hosts, thanks to 13-year-old Erraid Davies.
In the women's 100m freestyle, world champion Cate Campbell looks on course for gold as she qualified fastest for Monday's final in a time of 53:19sec.
Cate's sister Bronte was second fastest with Halsall down in fifth, although she appeared to be reserving herself for her bid for 50m butterfly gold later in the evening.
The intense competition for medals in the men's breaststroke events will also continue on Monday in the 50m final.
World record holder Cameron van der Burgh qualified fastest ahead of 19-year-old English sensation Adam Peaty.
However, after losing out to Peaty for gold in the 100m on Saturday, Van der Burgh is refusing to get his hopes up.
"I've been focusing more in the 100m and 200m. The 50m I have been neglecting. The most important thing is just to win, so we will see tomorrow night," said the South African.
"The 100m was a bit of a disappointment. I was looking forward to setting a personal best,” he added.
Another South African Chad le Clos, meanwhile, remained on course for double butterfly gold as he qualified second fastest for the 100m final after his victory in the 200m on Saturday.


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