Nawaqanitawase, who has won 11 caps for Australia since making his debut on last year's tour of Europe, will join the Roosters on a two-year deal.
The defection of one of their brightest rising stars is a big loss for Rugby Australia (RA) at a time when the code is under increasing scrutiny following a hugely disappointing World Cup campaign.
"We are disappointed, Mark has been a strong player over the last 12 months," RA chief executive Phil Waugh said in a statement on Thursday.
"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."
Despite the player not moving to rugby league until the season after next, RA appeared to close the door on him appearing for the Wallabies in the interim.
"Rugby Australia wishes to thank Nawaqanitawase for his efforts in his 11 Test appearances, as well as for the Waratahs and the Australia Sevens team at the Commonwealth Games," the organisation said in a statement.
The silver lining is that the winger's two-year contract with the Roosters offers the possibility of a return to rugby union ahead of the World Cup in Australia in 2027.
His code-switch will prevent him from facing the British and Irish Lions in 2025.
Nawaqanitawase's move follows months of back and forth between RA and the Roosters, who were furious when Joseph-Aukuso Suaalii was wooed to rugby union by recently ousted RA chairman Hamish McLennan.
RA also tried to sign Roosters back-rower Angus Crichton but that move fell over after the Origin forward's camp became increasingly frustrated with the governing body's negotiating tactics.
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