Captain Daniel Baier struck in the final minute of normal time to inflict a massive blow on Schalke's top four hopes.
The goal does, however, mean that the WWK Arena outfit will be a Bundesliga side next year.
Goalless at the break
As Horst Heldt was given a send off for his time as sporting director, Schalke started fastest on a sunny Saturday afternoon. A move through the heart of the Augsburg defence provided the first opening, although Joel Matip - who has found himself in odd positions in recent weeks - was brilliantly denied by Marwin Hitz.
Max Meyer was next to try his luck and suffered a similar fate to Matip, with his second attempt flying narrowly over the bar from the edge of the area. Huntelaar then came closer still, rattling the post with a 30-yard free-kick that curled just too much. Augsburg then had a chance of their own through Alfred Finnbogason but he headed wide.
Late goals see the game end level
The second half saw both teams tighten up and the game became much less open. Raul Bobadilla was a lick of paint from giving Augsburg the lead with a speculative shot from range, while Roman Neustädter had a powerful header palmed away by Hitz.
Then, suddenly, Schalke sprung a surprise and went ahead in the dying minutes. A superb move saw the host work the ball forward through Meyer, who gave the ball to Choupo-Moting to spread wide for Junior Caicara. The right-back whipped in a great ball towards the near post, and Huntelaar got the necessary contact to deflect it home.
Just as the game looked to be ending with Schalke claiming all three points, Daniel Baier had other ideas. He picked up a pass in space - around 20 yards from goal - and wasn't closed down by the home defence, allowing him to pick his spot and fire into the bottom corner; parity restored, points shared.