The Englisman steered his No. 22 McLaren Mercedes driver around the nearly three-mile Hockenheim Ring road course in one minute, 15.666 seconds, beating Ferrari's Felipe Massa by nearly a minute.
It gave Hamilton his third pole this season and ninth of his F1 career.
"My final lap went very smoothly," Hamilton said. "The wind was very strong and I felt it on blowing from the right and the left on the main straight."
Massa's time was 1:15.859.
Heikki Kovalainen (1:16.143) and Jarno Trulli (1:16.191) will start on Row 2, with 2007 F1 points champion Kimi Raikkonen of Ferrari securing the sixth position.
Raikkonen, Hamilton and Massa are locked in a three-way tie for the top spot in the latest driver standings.