The 23-year-old informed Rugby Australia (RA) that he will be leaving the 15-a-side code at the end of 2025 after he signed a one-year contract extension with the governing body and his Sydney-based club earlier this year.
The Sydney Roosters confirmed the news via their official website with he club's head of recruitment, Daniel Anderson, saying: "We're delighted to have secured Mark's services and look forward to welcoming him to our club in 2025.
"In the meantime, we wish him all the best for a successful 2024 in rugby union."
Meanwhile RA chief executive Phil Waugh expressed his disappointment in Nawaqanitawases decision.
"We are disappointed - Mark has been a strong player over the last 12 months," he said in a statement. "However, the outside backs are a position of strength for us, with great depth coming through.
"We are confident we are well-stocked with talented wingers for the future."
Nawaqanitawase burst onto the scene at Super Rugby level for the Waratahs in 2020 and made his international debut in a 28-27 loss to Italy in Florence during the Wallabies end-of-year tour of Europe in 2022.
Since then, he has established himself in Australia's first choice starting line-up and has already won 11 Test caps.
Nawaqanitawase was one of the Wallabies' standout performers during their recent woeful Rugby World Cup campaign in France where they failed to advance to the global showpiece's knockout rounds for the first time in the tournament's history.
He represented his country in six matches in 2023 and scored tries in the Wallabies' first two matches at the Rugby World Cup against Georgia and Fiji.
His departure to rugby league is offset by the arrival of Joseph Suaalii, who is joining the Waratahs in 2025, along with Sydney Roosters team-mate and Fijian rugby league international Vuate Karawalevu, who played in Waratahs' recent trials against New South Wales Pacifica.
Nawaqanitawase is expected to leave the door open for a return to rugby union in time for the 2027 Rugby World Cup which will be held in Australia.