The party's candidate, Manuel Brown, had secured nearly 70 per cent of the two-candidate preferred vote for the territory seat of Arafura by late on Saturday evening, beating the Country Liberal Party's Leslie Tungatalum.
Northern Territory Chief Minister Natasha Fyles congratulated Mr Brown on the victory and thanked volunteers and other supporters for their efforts.
"And to Manuel - let's get to work," she said in a Facebook post.
Mr Brown previously told AAP that improving roads, housing and health outcomes for residents were his biggest priorities.
Both he and rival Mr Tungutalum have roots in the Tiwi Islands, although Mr Brown currently lives in Arnhem Land.
Mr Brown received around two-thirds of first-preference votes, while just under 30 per cent went to the CLP candidate. The remainder went to Federation Party candidate Alan Middleton.
The vast electorate, which spans 57,000sq km, includes remote areas with large Indigenous populations like Arnhem Land, Kakadu and the Tiwi Islands.
The NT Electoral Commission's mobile polling team used four-wheel-drive vehicles and helicopters to get to remote towns, communities and outstations across the sparsely populated region.
The by-election follows the sudden death of the sitting Labor member, whose name AAP has not used for cultural reasons, in December.
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