Jan Rosenthal scored twice, but later became one of five players sent off in Saturday's six games, as Freiburg came from behind to extend Schalke's winless run to six league games.
The only consolation for their fiery coach, Huub Stevens, was sports director Horst Heldt's promise on Thursday that the Dutchman's job is safe for the time being.
Kiessling's brace made the unsung striker the Bundesliga top scorer with 12 goals. Andre Schuerrle was also on target as second-placed Leverkusen cut Bayern Munich's lead at the top to nine points at the Bundesliga's halfway mark.
Bayern slipped up on Friday when they were held 1-1 at home by Borussia Moenchengladbach, only the fourth time this season they have failed to win.
Promoted Eintracht Frankfurt went third with a 2-0 win after some early drama at VfL Wolfsburg. Alexander Meier and Takashi Inui scored for Eintracht while Wolfsburg had Josue sent off for a studs-up challenge, all in a six-minute spell before the 20th minute.
Greuther Fuerth and Augsburg both finished with 10 men as they drew 1-1 in a meeting of the bottom two, leaving them level on nine points from 17 games at the foot of the 18-team table.
Sascha Moelders gave Augsburg an early lead and Lasse Solbiech levelled after the break for Fuerth, who are in the Bundesliga for the first time and have yet to win at home.
Fuerth's Mergim Mavraj was dismissed for a second bookable offence, and his sending off was followed by that of Augsburg substitute Giovanni Sio, who got a straight red after only four minutes on the field.
Two goals from Nicolai Mueller helped Mainz 05 to a 3-1 win over VfB Stuttgart and promoted Fortuna Duesseldorf beat Hanover 96 2-1.
Kiessling has been among the Bundesliga's leading scorers over the past few seasons but has won only six caps for Germany, finding himself overshadowed by Miroslav Klose and Mario Gomez.
Leverkusen reached the halfway mark with 33 points, compared to Bayern's 42, with Frankfurt a further three points behind.
Leverkusen's progress has gone almost unnoticed with Bayern hogging the limelight, and Schuerrle said they did not expect to mount a challenge, despite the Bavarians' recent tendency to cave in at crucial moments of a campaign.
"Bayern are simply too good this year, we have to accept that," Schuerrle told reporters.
"But we want to cut their lead as much as possible and, naturally, we won't want to give up on second place."
Leverkusen went ahead when Kiessling side-footed past Rene Adler from an unmarked position in the 26th minute after Gonzalo Castro deflected the ball into his path.
Ten minutes later, Kiessling threaded a ball into the area for Schuerrle, who burst past his marker and shot past an exasperated Adler, who was again exposed by his defenders.
Adler was angrier at Leverkusen's final goal, in the 66th minute. Leverkusen goalkeeper Bernd Leno sent a long kick upfield that Heikko Westermann should have cleared, but instead he miscued, allowing Kiessling to go through and lob Adler.
Schalke dominated the early stages and Peru forward Jefferson Farfan gave them a deserved 20th minute lead.
But it quickly turned sour as Rosenthal replied in the 26th minute and Jonathan Schmid put them ahead six minutes later, scoring after Joel Matip miscued the ball.
Freiburg's third, in the 61st minute, came after Schalke lost possession playing their way out of defence and Rosenthal fired a stunning shot past Timo Hildebrand.
But Rosenthal turned villain when he was booked twice in quick succession, and a minute later Schalke forward Klaas-Jan Huntelaar was also dismissed for lashing out at a defender in the penalty area.
"We started well and deservedly took the lead," Heldt told Sky Sports at halftime. "Then we stopped going forward. That has happened to us frequently this season."
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