Marquez, who leads the world championship by 72 points having won every race this season, broke the mark set in 2008 by Casey Stoner with a lap of one minute and 20.937 seconds.
Repsol Honda rider Marquez snatched top spot on the grid from team-mate Dani Pedrosa (1:21.233), who crashed at turn one with three minutes of the session remaining.
LCR Honda's Stefan Bradl (1:21.340) delighted the home crowd in Saxony as the German capped off the front row.
Marquez's closest challenger Valentino Rossi (1:21.651) could only claim sixth behind NGM Forward Racing's Aleix Espargaro (1:21.376) and Movistar Yamaha team-mate Jorge Lorenzo (1:21.508).
Bradley Smith (1:21.794) suffered his fourth fall of the weekend, but the Brit was still to complete row three by taking ninth for Monster Yamaha Tech 3
Smith's team-mate Pol Espargaro (1:21.771) is ahead in eighth, just adrift of Pramac Racing's Andrea Iannone (1:21.679).
Andrea Dovizioso and Nicky Hayden qualified 11th and 12th after progressing from the first qualifying session, which saw Cal Crutchlow left to settle for 15th following a fall.