The Honda rider's time of one minute 20.270 was a track record and left him perfectly placed for a ninth win in a row on Sunday at the eastern circuit near Chemnitz.
The Spaniard was pushed hard by Pramac Ducati's Italian Danilo Petrucci, who lapped only 0.025 seconds slower. Petrucci was also second fastest in qualifying last year.
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Spaniard Jorge Lorenzo, who will be Marquez's team mate next season, completed the front row for Ducati.
Yamaha's Maverick Vinales qualified fourth with two Italians -- Ducati's Andrea Dovizioso and Yamaha's Valentino Rossi joining him on the second row.
Marquez's run of poles at the Sachsenring started in 2010 when he was competing in the 125cc category (now Moto3). He then took pole in Moto2 in 2011 and 2012 and is on a sequence of six in MotoGP.
The 25-year-old four-times MotoGP world champion won all of those races. He is currently 41 points clear of Rossi in the championship after eight rounds.
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