Cameroon internationals Joel Matip and Eric Maxim Choupo-Moting scored for Schalke, who host Maribor in the Champions League on Tuesday, before Pierre-Emerick Aubameyang pulled one back for the visitors.
Schalke moved up to seventh on eight points while last season's runners-up Dortmund, who take on Anderlecht in the Champions League, slipped to ninth, a point behind following their third loss in six league games.
The win also eased pressure on Schalke boss Keller, with his team now winning two in a row after picking up just two points in their first four games.
"We are over the moon because a derby is something special and to win at home in front of our fans is just wonderful," said Keller. "Despite the fact that Dortmund's goal put a dent in our performance, the boys hung in and fought until the end."
For Dortmund counterpart Juergen Klopp's team it was their third league game without a win, having lost two of them as they dropped seven points behind leaders Bayern Munich.
With captain Mats Hummels making his first start of the season but without their entire first-choice midfield, Dortmund were on the backfoot from the start.
Hummels, who had not played since the World Cup final until the 2-2 draw against VfB Stuttgart in midweek, looked out of position when unmarked Matip rose among four Dortmund players to head in on 10 minutes.
Dortmund keeper Roman Weidenfeller then did well to block a Klaas-Jan Huntelaar effort but his defence let him down again with Cameroon international Choupo-Moting drilling in on the rebound in the 23rd minute.
Dortmund's Aubameyang cut the deficit three minutes later but despite a strong second-half performance they failed to get an equaliser.
"This is not a good situation for us," said fellow central defender Neven Subotic. "But it is up to us get ourselves out of it."
AWAY WIN
Bayern Munich, who travel to CSKA Moscow on Tuesday, extended their lead at the top with a patient 2-0 win over promoted Cologne, who were lucky not to concede more as Xabi Alonso set a league record for most touches in a game with 204.
Mario Goetze continued his scoring run with his fourth goal of the season and Daniel Halfar fired in an own goal in the 66th minute to lift the champions to 14 points, two ahead of Borussia Moenchengladbach, who eased past promoted Paderborn 2-1, scoring twice in the opening 14 minutes.
Coach Pep Guardiola was happy with their first away win of the season, especially with the Moscow game looming.
"It was not easy although we did control the game, never dropped our guard and allowed very few counter attacks. Now we will sleep here in Cologne and fly to Moscow tomorrow," said the Spaniard.
Ten-man Bayer Leverkusen, who had defender Emir Spahic dismissed in the 30th minute, rescued a draw at Freiburg, who also ended the game with 10 men. Leverkusen, who host Benfica in the Champions League next week, are third on 11 points.
Former champions Stuttgart notched their first win of the season under new coach Armin Veh with a 1-0 over Hanover 96 with Daniel Schwaab's goal enough to lift them away from the bottom spots.
(Editing by Ed Osmond and Toby Davis)
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