MORE: Commonwealth Games medal table
In Australia's best day yet at the Games with eight gold medals claimed, Magnussen touched the wall first at 48:11 in a historic Aussie trifecta as national champion Cameron McEvoy and Tommaso D'Orsogna won the minor medals.
It was Magnussen's first individual Commonwealth Games gold medal to go with the 4x100 freestyle victory on Friday.
The 23-year-old was knocked off his perch in the national titles by McEvoy in April and was pleased that the plan cooked up by coach Brant Best had paid dividends.
"Having a loss at trials was not ideal so I just wanted to get the win tonight to reaffirm to myself that I've still got it and am still going good and now I can focus on getting the quickest race I can against the Americans at Pan Pacs (in late August) because they'll bring some more heat again," Magnussen said.
"At the end of the day it's a pretty simple sport, whoever touches the wall first gets the gold medal and Brant and I devised what we thought was a bullet proof plan and it worked, so it was really, really simple."
Australia's queen of the velodrome, Anna Meares, had to pass on her crown as housemate Stephanie Morton upstaged the veteran in the women's sprint final.
Amid rumours of a possible retirement, Meares explained that the result was not out of the blue.
"She's been serving me humble pie all year so it's certainly not a big shock to the system," Meares said.
"Sometimes you get beaten."
Aussie swimmer Belinda Hocking finally had a breakthrough as she claimed gold in the women's 200 backstroke ahead of compatriot Emily Seebohm.
Hocking got to the wall first in a Games record time of 2:07.24, with Seebohm grabbing silver in 2:08:55.
There were also Australian gold medals in the pool for Ben Treffers (50m backstroke) and the 4x200m freestyle relay team.
Michael Shelley claimed gold medal in the men's marathon - holding off Kenyan favourite Stephen Chemlany while Michael Glaetzer won the men's keirin cycling gold.
In other Commonwealth Games news, Kenya's Caleb Ndiku won the first track medal of the Glasgow Commonwealth Games on Sunday as he took gold in the 5000 metres.
The world indoor champion held off competition from compatriot Isiah Koech and New Zealand's Zane Robertson to win in 13 minutes, 12.07 seconds.
With Olympic champion Mo Farah absent due to illness, Robertson and brother Jake led the early running before the Kenyans took charge - Ndiku finishing almost two seconds clear of Koech.
England's Fran Halsall became the first woman to complete a Commonwealth sprint double in the pool, adding the 50m butterfly title to her freestyle crown over the same distance by finishing 0.33secs clear of Arianna Vanderpool Wallace.
Siobhan O'Connor added 200m individual medley gold to the three bronze medals and one silver she had already claimed for England at the Games, while Ben Treffers headed an Australian one-two in the 50m backstroke ahead of Mitch Larkin.
Sophie Pascoe of New Zealand took gold in the final of the 100m breastroke SB9 contest.
There was a big shock in the rugby sevens at Ibrox as reigning champions New Zealand were beaten by South Africa.
The Kiwis have won gold at the last four Games but came up short in a 17-12 defeat after Australia had been dominant in picking up bronze against Samoa.
In the women's fours lawn bowls, South Africa recovered from 9-4 down after nine ends against Malaysia to eventually prevail 14-9.
New Zealand's Jo Edwards saw off defending Commonwealth champion Natalie Melmore 21-15 in the women's singles.
The women's section of the 63kg Group A weightlifting was won by Olauwatoyin Adesanmi with a total weight of 207kg, while India's Sathish Sivalingam lifted 328kg on his way to gold in the men's 77kg contest.