The key defender and midfielder finished the count locked on 50 votes to share the Roos' coveted Syd Barker Medal, one vote clear of ruckman Todd Goldstein with vice-captain Drew Petrie fourth, three votes further back.
It was Thompson's first best and fairest win and followed his runner-up finishes in 2009 and 2012, while Wells shared the club's top individual honour for the second time, following his tie with North captain Andrew Swallow in 2011.
In a year when he earned his first All Australian selection, Thompson also took home the Harold Henderson Best Clubman honour awarded by North's coaching team.
Earlier in the night, Wells and veteran defender Michael Firrito were awarded North life membership.
Vice-captain Jack Ziebell was another of the night's big winners, taking home the Jason McCartney Jumper Award, the Glenn Archer Northerners Award and the Blackwoods Supporters Player of the Year Award.
Former rookie and Rising Star nominee Aaron Mullett was named Best First Year Player after spending his first full year on North's senior list, while leading goalkicker Lindsay Thomas was recognised for his off-field work with the Peter Scanlon Community Award.
Syd Barker Medal top 10
1. Scott Thompson 50
1. Daniel Wells 50
3. Todd Goldstein 49
4. Drew Petrie 46
5. Ben Cunnington 45*
6. Ryan Bastinac 45*
7. Jack Ziebell 43
8. Lachie Hansen 41*
9. Sam Gibson 41*
10. Aaron Mullett 40
*Countbacks apply for all placings other than first
Glenn Archer Northerners Award – Jack Ziebell
Blackwoods Supporters Player of the Year Award – Jack Ziebell
Jason McCartney Jumper Award – Jack Ziebell
Best First Year Player – Aaron Mullett
Harold Henderson Best Clubman Award – Scott Thompson
Peter Scanlon Community Award – Lindsay Thomas