Pendlebury, 22, finished with a team-high 29 possessions (12 contested) and five clearances, and booted a goal in the third term.
Youngster Dayne Beams came equal second in the voting, with a massive 13 inside-50s including four in the first term when Collingwood set up the win.
Cloke booted four goals in the first half, including three as the Pies scorched to a virtually unassailable 44-point lead at the first change.
"I was a little bit surprised," Pendlebury said on receiving the medal after the match.
"I thought Clokey set us up early, especially the way he played and kicked goals.
"He kicked a few good goals too, and he set the tone for us, even with a few of his tackles in the forward 50 that allowed other guys to get goals as well.
"So I thought Clokey was a little bit stiff."
The Bombers worked hard in the second quarter to prevent the lead ballooning any further, but the Pies booted six goals to two in the third term to nail the coffin lid shut.
Pendlebury said the win was the Pies' most complete performance for the year.
"It's fantastic - I think the way we played all day was really set up by the way we played that first quarter," he said.
"And then to keep going that way, and to keep applying the pressure and doing all those little things, attitudinal things, when you're up by that much was fantastic."
How they voted
Stan Alves (ABC)
3 Scott Pendlebury (Collingwood)
2 Harry O'Brien (Collingwood)
1 Heath Shaw (Collingwood)
Shane Crawford (Triple M)
3 Dayne Beams (Collingwood)
2 Alan Didak (Collingwood)
1 Scott Pendlebury (Collingwood)
Anthony Hudson (SEN)
3 Sharrod Wellingham (Collingwood)
2 Scott Pendlebury (Collingwood)
1 Travis Cloke (Collingwood)
Total
6 - S Pendlebury
3 - D Beams, S Wellingham
2 - A Didak, H O'Brien
1 - H Shaw, T Cloke
