The result was about a six per cent swing towards the ALP from the last election, making the seat now the safest ALP electorate in the NT.
"We will continue to work with, and engage the community in this period of change."
Commentators had thought it would be tough for the CLP to win Wanguri, which Labor has held since 1989, particularly after recent 30 per cent electricity price hikes and government cutbacks.
The CLP had said the price rises were needed to alleviate the debt held by the public-owned Power and Water Corporation.
But Ms Manison said the result was Territorians sending Mr Mills a message he couldn't ignore.
"People are unhappy with his broken promises and unfair price hikes," she said.
The by-election was sparked by the resignation of former chief minister Paul Henderson.
Counting will continue on Sunday with about 89 per cent of the vote counted so far.