"Witness" was shot in a single take at salt lake The Pool of Siloam in South Australia's Beachport.
The Ramsay Prize, awarded at the Art Gallery of South Australia on Friday, is Australia's biggest award for artists under 40 and comes with the same prize money as the Archibald Prize.
Sophia is a former student at the Marina Abramovic Institute in Greece, where she studied the methods of the world's most famous performance artist.
In the winning artwork, Sophia is repeatedly submerged and lifted out of the water as a way of examining baptism and what the artist sees as its painful consequences.
The Adelaide artist, 34, saw her father baptised as a young child and said she felt he loved Jesus more than he loved her.
"Despite being agnostic, I responded by pretending to be incredibly devout, blindly seeking to regain his love," she said in an artist's statement.
Sophia chose South Australia's Pool of Siloam because it is where she swam as a child and is named after a biblical site where Jesus is said to have restored a man's sight, reflecting her attempts to "see" Christ like her father did.
The performance and video show actions of vain hope can be exhaustive, violent and ultimately futile, she said.
"Ida Sophia is clearly at a pivotal point in her career - her winning work Witness is technically and conceptually resolved, capturing the breadth of her practice to this point," gallery director Rhana Devenport said.
The Ramsay Art Prize 2023 exhibition runs from Saturday until August 27 at the Art Gallery of South Australia.
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