The Spaniard, who has won all eight races this season, slipped off his Honda at Turn Three during the morning session but returned in the afternoon to post the second fastest time.
The quickest time belonged to his compatriot Aleix Espargaro whose Yamaha clocked one minute, 22.041seconds, around the Sachsenring circuit.
Marquez, the reigning world champion who leads this year???s campaign by 72 points, crossed the line in a time 0.117 seconds slower than Espargaro.
Jorge Lorenzo, another Spaniard, was third quickest ??? 0.327s off the pace ??? while Valentino Rossi and Dani Pedrosa who share second place in the overall standings were sixth and 10th respectively.
The latter walked away unhurt from a high-speed crash at Turn 12 during the afternoon.
Another to slip from his machine was Briton Bradley Smith who fell off twice in the morning but still managed to register the 11th best time ?????0.678s behind Espargaro.
The top 16 riders, which include three other Brits ??? Cal Crutchlow (13th), Michael Laverty (14th) and Scott Redding (15th) ??? are separated by less than a second at the short, tight and twisting track which used to stage the East German Grand Prix.