Magnussen was beaten by McEvoy in the 100m final on Tuesday but got his hand on the wall first to win the one-lap sprint at Sydney's Olympic pool.
Magnussen won in a time of 21.98 seconds, just 0.05 ahead of McEvoy, who was bidding to become the first man to win the 50m-100m-200m freestyle treble at the Australian championships.
"Even though I lost the 100m, it didn't really knock my confidence," said Magnussen. "It is still only early stages."
Emily Seebohm completed the women's backstroke treble when she took the 200m final in 2:06.69, the fastest time in the world this year.
Tommaso D'Orsogna won the men's 100 butterfly, Jessica Ashwood (8:26.09) took the women's 800m freestyle and Brittany Elmslie (26.07) claimed the women's 50m butterfly title.
The Australian championships are doubling as the country's trials for this year's world championships in Kazan, Russia.
(Writing by Julian Linden in Singapore; Editing by Peter Rutherford)
Share
