Padernal accumulated a total of 1,210 points to unseat 2004 MVP Wendell Zamora of Transco, who had 1,060.
The points they earned came from all the leagues MCTTL organized this year.
Little known Carl Ardiente of PAGCOR was third overall with 1,025 points.
MCTTL's 2nd anniversary champion Jason Cabahug settled for fourth place with 775 points and University of the Visayas' Ian Sabalo was fifth with 690 points.
The sixth to 10th placers were Orville Tecson of Cebu Institute of Technology with 600 points, USJ-R's Quent Quroljico (535 points), GAB's Darin Gavan (525 points), Recovery House's Rock Olofernes (500 points) and UV's Jeffrey Kuizon with 495 points.