Jones won 10 of his 12 games in charge after replacing Gary Megson at Sheffield Wednesday in February to steer the Owls to automatic promotion.
The former Southampton and Cardiff boss, unbeaten as Wednesday manager, finished ahead of Reading's Brian McDermott in the table, while Sir Alex Ferguson was third.
The Castrol LMA managers' performance table was devised to allow managers from every level of League football to test themselves against one another.
Every competitive game counts towards a manager's individual score in the League. Points are awarded for victories and draws, with results away from home scoring higher.