Spaniard Marquez, 20, never looked back after taking the lead on the sixth of the 30-lap race. Britain's Cal Crutchlow was second and nine-times world champion Valentino Rossi was third.
Pedrosa, who suffered a minor fracture to his collarbone after crashing during practice on Saturday, was cleared to take part in Sunday's warmup but felt unwell and withdrew with low blood pressure.
He dropped to second in standings, two points behind Marquez, who is on 138.
Jorge Lorenzo, the reigning world champion, also missed the race at the Sachsenring after crashing on Friday, leaving him third in the championship.