Mario Gomez fired in from inside the box after a fine solo effort after 35 minutes with Thomas Muller doubling their lead midway through the second half before Hakan Balta's goal 11 minutes from time gave the hosts some brief hope.
Bastian Schweinsteiger, however, sent keeper Volkan Demirel the wrong way as he converted an 86th minute penalty and secured the win for his team.
"Compliments to the players," Germany coach Joachim Loew told reporters. "We held our own in this stadium and this atmosphere. To beat a team that is highly motivated in front of 50,000 of their own fans is quite an achievement."
"Our aim is to win 10 games out of 10. The aim is to win, not to give Turkey a present," he said.
Already qualified for next year's tournament, Germany are eager to become the first team from their country to win 10 out of 10 qualifiers for a major tournament. They top Group A on 27 points with their last game next week against Belgium, who moved up to second on 15 with a 4-1 win against Kazakhstan.
Muller made amends in the 65th minute for an earlier miss connecting with a Mario Gotze pass to thunder in from the right for Germany's second goal
Guus Hiddink's Turkey came back and cut the deficit in the 79th with Balta firing a Gokhan Gonul pass but Schweinsteiger dashed any hopes, converting the penalty awarded after Muller was brought down in the box.
"Yes of course. Because we have to win on Tuesday and Germany will have to beat Belgium. We believe we will reach the play-offs because there cannot be any surprises at these games," he told reporters.
