Pendlebury capped an outstanding season to claim his second Magpies best and fairest, which accompanies his fourth consecutive All Australian selection.
The 25-year-old polled 192 votes ahead of three-time winner and runner-up Dane Swan (155), with 22-year-old Steele Sidebottom (133) rounding out the top placegetters in third.
Pendlebury also received the Darren Millane Memorial Trophy as Best Clubman – further enhancing his captaincy credentials.
The star midfielder averaged a career-high 29.9 disposals per game in 2013, while ranking second in the competition for disposals (688), sixth in clearances (131) and ninth in contested possessions (290).
Swan achieved his sixth top-three finish in a row, in a season where he placed third in the Brownlow, earned his fifth All Australian selection and led the AFL in disposals.
The star on-baller claimed the RT Rush trophy as runner-up, and also won the Bob Rose Award as the club's best finals player.
Sidebottom's emergence was rewarded with the highest finish of his career in taking out the J.J. Joyce Trophy.
Magpies spearhead Travis Cloke was fourth and won the McHale Trophy, while the dashing Harry O'Brien put a difficult year behind him to round out the top five with the Jack Regan Trophy.
2013 Copeland Trophy top 10
1. Scott Pendlebury - 192 votes (E.W Copeland Trophy)
2. Dane Swan - 155 (R.T Rush Trophy)
3. Steele Sidebottom - 133 (J.J Joyce Trophy)
4. Travis Cloke - 108 (J.F McHale Trophy)
5. Harry O’Brien - 101 (Jack Regan Trophy)
6. Brent Macaffer - 76
7. Marley Williams - 70
8. Heath Shaw - 69
9. Nathan Brown - 61
10. Jamie Elliott - 59
Joseph Wren Trophy (VFL Best and Fairest Player) – Kyle Martin
Darren Millane Memorial Trophy (Best Clubman) – Scott Pendlebury
Harry Collier Trophy (Best First Year Player) – Josh Thomas
Gordon Coventry Trophy (Goal Kicking Award) – Travis Cloke
Gavin Brown Award (Leading Desire Indicators) – Jarryd Blair
Bob Rose Award (Best Finals Player) – Dane Swan
Magpie Army Player of the Year – Dane Swan