Die Knappen saw off the Breisgau outfit thanks to a fine display by the young German playmaker and secured their spot in the Bundesliga top four as a result
Julian Draxler opened the scoring in the 20th minute with a fine shot from 15 yards out to put his team in the lead.
Jan Rosenthal then made the best out of a Timo Hildebrand rebound in the 54th minute to equal the scoring, only to get cancelled out by a Julian Schuster own goal shortly afterwards.
Fourth-placed Schalke went into the match with a one-point advantage over the home team, as both sides were looking to secure the final Champions League qualification spot.
The fired-up atmosphere in Freiburg was certainly suitable for the last matchday with so much being at stake and it reflected with the players on the pitch.
Both sides looked lively from the beginning and were equally hungry to win the game. Early into the match, Immanuel Hohn lurked near the far post and caused an early, major scare for the visiting side, as he wasted a huge opportunity to get ahead in the sixth minute after a fine cross by Jan Rosenthal.
However, despite an ambitious showing by the Breisgau outfit, the guests broke the deadlock in the 20th minute, when Germany international Draxler accurately placed the ball in the right-hand corner of the box from outside the area, leaving Oliver Baumann no chance to save.
As the match was nearing the break, Christian Streich's side dominated possession, trying to seize opportunities up front as S04 focused their game on counterattacks, but a solid defensive display by the hosts prevented them from carving out any big chances.
Raffael sparked up the good opportunity before heading into the locker room, when he worked his way towards the target before unleashing a powerful strike, which went over the bar.
Then, after a corner for the guests early in the second half, Jonathan Schmid intercepted the ball, sprinted towards the Knappen goal and found Max Kruse on the left side. Timo Hildebrand deflected his effort directly on to Rosenthal's feet and the midfielder did not hesitate when he blasted the rebound into the box.
But, not five minutes later, Schalke restored their lead with help from Julian Schuster. Jermaine Jones ran down the right flank and crossed into the midfielder's path, who then recorded his first-ever Bundesliga own goal after trying to clear the ball.
Shortly after, Klaas-Jan Huntelaar had the chance to extend the advantage after Draxler provided him with a fine pass, but the Oranje star missed the target by an eyelash with his curl towards the right corner of the net.
Freiburg created some good chances in the dying minutes as well but ultimately could not change the result in their favour.
Die Knappen remain fourth and seized the opportunity to qualify for the play-off round before the group stages of the Champions League next term, while Freiburg look forward to their third-ever appearance in the Europa League.