Joachim Low's side, who made sure of their place in South Africa next summer thanks to Saturday's 1-0 win in Russia, fell behind to Jonatan Johansson's early strike.
Despite long spells of pressure, it seemed as though Germany were going to suffer their first defeat in qualification only for Lukas Podolski to scramble home a late, scrappy equaliser.
Low said afterwards: "For sure, we did not play well in the first half.
"We could not create many chances and allowed a lot of counter-attacks.
"In the second half we showed our strong morale to not lose this game, and had some good chances."
Russia, who were already certain of a place in the play-offs were also held, 1-1 in Azerbaijan.
Andrei Arshavin scored for Russia with Vagif Javadov grabbing the leveller.
The visitors could have claimed all three points late on but Sergei Ignashevich's penalty was saved by Azeri keeper Kamran Agaev.
The other game in Group Four saw Wales win 2-0 in Liechtenstein.
The match, a dead rubber for both teams, was a low-key affair with the Welsh claiming the win thanks to goals from David Vaughan and Aaron Ramsey.