Freiburg coach Christian Streich let out a primal scream at the final whistle as his team go into the winter break in their highest position in the club’s history.
The 20-year-old Schade came off the bench and stole a march on Leverkusen goalkeeper Lukas Hradecky at a corner to tap the winner into the net six minutes from time.
“We really wanted to be third over the festive period,” goal-scorer Vincenzo Grifo told DAZN.
“When we look at the table over Christmas, it makes for good reading.”
Freiburg took the lead at their Europa Park Stadium in Germany’s Black Forest when Italy forward Grifo chipped in a first-half penalty.
Leverkusen equalised just before the break when Germany defender Jonathan Tah hooked a pass to Charles Aranguiz who headed past the Freiburg goalkeeper.
However, with time running out Schade ghosted in front of Hradecky and flicked the ball into the net to the despair of the Leverkusen goalkeeper.
Freiburg’s defence has conceded a club-record low of 16 league goals in the first half of the season.
The hosts’ defence worked tirelessly to contain Leverkusen striker Patrik Schick who scored eight goals in his previous three Bundesliga games.
Freiburg’s win saw them leap-frog Leverkusen into third spot, 14 points behind Bundesliga leaders Bayern Munich.
The Bavarian giants are on course to win a tenth straight Bundesliga title and start the two-week winter break nine points clear at the top of the table after Friday’s 4-0 thrashing of Wolfsburg.
Second-placed Borussia Dortmund blew the chance to trim Bayern’s huge lead on Saturday when they slumped to a 3-2 defeat at Hertha Berlin.