Christian Clemens drilled in the winner from 20 metres for the hosts after 21 minutes with fourth-placed Gladbach only turning up the heat in the second half.
The visitors missed a golden chance through Raffael, who saw his close range effort spectacularly blocked by goalkeeper Loris Karius.
Gladbach remain on 29 points, after also losing 3-1 to Borussia Dortmund last week, while Mainz move up to sixth on 27 with their first win of the year.
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Schubert's side, hit by a string of injuries this term, had won six consecutive games after he took over, following five defeats in a row at the start of the campaign, taking them off the bottom and into Champions League contention.
But after winning eight of 10 league matches under the 44-year-old, they have yet to pick up where they left off before the winter break in December.
Leaders Bayern Munich, who have 49 points, host Hoffenheim on Sunday, with second-placed Borussia Dortmund, eight points off top spot, entertaining promoted Ingolstadt on Saturday.
(Reporting by Karolos Grohmann; editing by Ken Ferris)
