That group was whittled down to 10 in strong cross winds as it neared the bottom of Bluff Hill and by the top just seconds split the field, with Northey taking stage honours three seconds ahead of Bissell Pro Cycling's Carter Jones and 25 seconds in front of Pure Black Racing's Taylor Gunman.
The win puts Northey into yellow, eight seconds up on Jones. Gunman, who will now wear The Co-operative Bank Under-23 jersey after a strong day, is third on the overall general classification.
"We'll have a bit of work to do on the front now and we'll just take every day as it comes," Northey said.
"We'll see how long we can stay in the top three - that's my goal, top three in GC, so we'll just see what happens."
Stage results: Michael Northey, Node 4-Subaru, 3:18:36, 1; Carter Jones, Bissell Pro Cycling, at 3sec, 2; Taylor Gunman (U23), Pure Black Racing, at 25sec, 3.
GC results: Michael Northey, Node 4-Subaru, 7:16:31, 1; Carter Jones, Bissell Pro Cycling, at 8sec, 2; Taylor Gunman (U23), Pure Black Racing, at 27sec.
Team results: Node 4-Subaru 21:45:01, 1; Bissell Pro Cycling at 17sec, 2; Calder Stewart and Pure Black Racing at 18sec, 3.
U23 results: Taylor Gunman (U23), Pure Black Racing, 3:19.01, 1; Cameron Karwowski, PowerNet, and Fraser Gough, Share the Road, at 16sec, 2.