Schalke 1 Hoffenheim 0
Andre Breitenreiter's side had conceded in stoppage time last weekend to lose 2-1 at Augsburg, which halted their two-match unbeaten run in the Bundesliga.
But they returned to winning ways against the struggling achtzehn99, with Choupo-Moting's goal on 28 minutes separating the two teams on the night.
Die Konigsblauen provisionally move into the final Champions League place ahead of the weekend's matches, while Huub Stevens' team remain in the relegation zone after suffering their eighth loss of the season.
Hoffenheim were guilty of failing to take their host of chances as they shaded the hosts in possession and shots taken, but only managed to test goalkeeper Ralf Fahrmann once in the entire match.
That was on 18 minutes when Nadiem Amiri forced a save out of Fahrmann with his strike from inside the area on the right after being picked out by Tarik Elyounoussi.
But it was Schalke who would break the deadlock just before the half-hour mark as Choupo-Moting turned home Johannes Geis' cross with his back to goal.
The closest either team came to adding to the scoreline in the first half was when Franco Di Santo connected with Geis' corner, but steered the ball just wide of the left post.
It was more of the same in the second half for the visitors as they carved out seven chances, but failed to hit the target on each occasion.
The woodwork then came to their rescue on 64 minutes as Sead Kolasinac saw his effort from an acute angle on the left came back off the near post to deny Schalke a second goal.
Leroy Sane forced Hoffenheim keeper Oliver Baumann into a rare save on 76 minutes with a header from Kolasinac's cross, while Fabian Schar wasted a chance to equalise in stoppage time when he guided the ball past the left post from Jonathan Schmid's pass.