Noakes landed the 35 - metre effort from the right flank to make it four wins from four for the Highlanders and take them back to the top of the New Zealand conference.
The Highlanders failed to reach the high level of play they had demonstrated in the three previous wins but were happy to e dge another close - fought game.
"Four wins, pretty happy, but obviously a lot to work on," Highlanders captain Jamie Mackintosh said in a pitchside interview.
"We really know how to close out a game, there was a lot of composure. Winning instils confidence."
The visitors started strongly and looked like they would win comfortably as All Black flyhalf Colin Slade stroked over two penalties , punishing the Hurricanes for routinely infringing in the opening stages.
Slade then dived over from close range for the first try of the match in the 16th minute after scrumhalf Jimmy Cowan's tap penalty and dart put them deep into Wellington's 22.
Slade swept over the conversion from in front of the posts to stretch the lead to 13-0 as the Highlanders looked like they were going to cut loose.
However, the Hurricanes emerged from their early slumber, flyhalf Beauden Barrett kicking a penalty after 29 minutes to get them on the scoreboard.
Barrett then kicked an easy effort two minutes later before his pinpoint pass set up All Black winger Cory Jane for the Hurricanes' opening try in the 37th minute.
Barrett then sent over his third penalty from 35 metres right on halftime to send the home side into the break 14-13 ahead.
Slade slotted another penalty nine minutes into the second half to put the Highlanders back in front 16-14 after the Hurricanes infringed at a ruck.
The Highlanders were well on top and thought they had their second try as winger Kade Poki crossed after a sweeping move but replacement referee ruled it out for a forward pass.
Barrett converted another penalty from 40 metres to put the Hurricanes ahead 17-16 with 11 minutes remaining before Noakes struck after the home side were guilty of not releasing the ball.
"We had a bit of trouble getting out of our own zone," Hurricanes captain Conrad Smith said after their second defeat in four matches.
"To be honest both sides struggled. We could have ended up winning but we still wouldn't have been happy."
Teams:Hurricanes:
15. André Taylor, 14. Cory Jane, 13. Conrad Smith (captain), 12. Tim Bateman, 11. Julian Savea, 10. Beauden Barrett, 9. TJ Perenara, 8. Victor Vito, 7. Jack Lam, 6. Faifili Levave, 5. Jason Eaton, 4. Jeremy Thrush, 3. Jeffery Toomaga-Allen, 2. Dane Coles, 1. Ben May
Substitutes: 16. Motu Matu'u, 17. Michael Bent, 18. James Broadhurst, 19. Brad Shields, 20. Chris Eaton, 21. Dan Kirkpatrick, 22. Charlie Ngatai
Highlanders:
15. Ben R Smith, 14. Kade Poki, 13. Tamati Ellison, 12. Phil Burleigh, 11. Hosea Gear, 10. Colin Slade, 9. Jimmy Cowan, 8. Nasi Manu, 7. John Hardie, 6. Adam Thomson, 5. Nick Crosswell, 4. Josh Bekhuis, 3. Ma'afu Fia, 2. Andrew Hore, 1. Jamie MacKintosh (Captain)
Substitutes: 16. Jason Rutledge, 17. Bronson Murray, 18. Culum Retallick, 19. James Haskell, 20. Aaron Smith, 21. Chris Noakes, 22. Buxton Popoalii