The Cowboys dominated from the opening whistle to race away to a 16-0 lead after 19 minutes of play. Souths got on the board with their first try in the 24th minute.
But the North Queenslanders struck back soonafter on the back of some driving defence and brilliant attacking play to post a 22-6 lead at the break.
The Cowboys continued to dominate after the break, winning all the stats and scoring five more tries to bring their match tally up to nine overall.
A well beaten side across the park, South Sydney found some consolation when they crossed for their second try in the final minute.
The victory is North Queensland's fourth in a row, and for the time being find themselves in fifth position on the NRL ladder. Next week they take on current competition leaders St George Illawarra Dragons in Wollongong.
The ninth-placed South Sydney will next week play host to the high flying Melbourne Storm in Perth.
Match Details North Queensland Cowboys 46 def South Sydney Rabbitohs 12 Round 13 - Saturday June 6th, 2009 07:30pm Venue: Dairy Farmers Stadium Referee: Shayne Hayne & Gerard Sutton Sideline Officials: Steve Chiddy & Adam Devcich Video Referee: Tim Mander Crowd: 16,568 Halftime: Cowboys 22-6
North Queensland Cowboys 46 Tries: John Williams (2), Ashley Graham (2), Aaron Payne, Scott Bolton, Matt Bowen, Ty Williams, Matthew Scott Goals: Johnathan Thurston (5/9) South Sydney Rabbitohs (12) Tries: Beau Champion, Craig Wing Goals: Chris Sandow (2/2)
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COWBOYS: 1. Matthew Bowen 20. Ty Williams 3. Ashley Graham 4. Willie Tonga 5. John Williams 6. Travis Burns 7. Johnathan Thurston (c) 8. Shane Tronc 9. Aaron Payne 10. Matthew Scott 15. Steve Southern 12. Scott Bolton 13. Luke O'Donnell Interchange: 11. Carl Webb 14. Anthony Watts 16. Antonio Kaufusi 18. Steve Rapira RABBITOHS: 1. Luke Capewell 2. Nathan Merritt 3. Colin Best 4. Beau Champion 5. Fetuli Talanoa 6. John Sutton 7. Chris Sandow 8. Luke Stuart 9. Issac Luke 10. Roy Asotasi (c) 11. Michael Crocker 12. David Fa