In other action on a night of just seven qualifiers around the continent, there were wins for Croatia, Russia, Ireland, Poland and Finland.
Cyprus, who stunned Ireland 5-2 last month for their most impressive ever international win, were not expected to get anything from their Group D match against the three-time world champions, even though the Germans were missing a number of injured key players.
Michael Ballack looked to have put Germany on their way to a fourth successive win in the group, marking his 75th appearance for his country with his 35th international goal after 15 minutes, but the gritty home side fought back with Yiannakis Okkas equalising just before halftime with a volley to complete the scoring.
In the other match played in the group, Ireland beat San Marino 5-0 in the last match to be played at Lansdowne Road before it is redeveloped with skipper Robbie Keane scoring a hat-trick for the home side.
The victory was Ireland's first in the group to lift them to four points, the same as Cyprus, but six points behind leaders Germany and the Czech Republic.
CROATIA TOP
Croatia also had a night to savour by becoming the first visiting team for seven years to beat Israel in Tel Aviv winning a thrilling match 4-3.
The victory lifted Croatia to the top of Group E with 10 points from their four matches, two more than Russia who won 2-0 in Macedonia.
Brazilian-born striker Eduardo da Silva was Croatia's hero with a hat-trick as the visitors recovered after conceding a soft early goal. They came back to lead 3-1 early in the second half, but Israel fought back to trail 3-2, then 4-2 -- before finally being beaten for the first time after 13 successive World and European qualifiers without loss since 2003.
Russia's goals in the victory over Macedonia came from Vladimir Bystrov and Andrei Arshavin in the first half to lift them into second place above England in the group.
FINLAND TOP
Finland, who have never qualified for the World Cup or European finals, moved to the top of Group A with a 1-0 win over Armenia while Poland moved above Belgium after beating them 1-0 in Brussels.
Portugal were facing Kazakhstan in a later match in the same group.
Mika Nurmela headed the only goal after 10 minutes to give Finland victory and take them top with 11 points from five matches, although they have played one more match than second-placed Serbia who have 10 points.
Poland won a crucial game in Brussels by the same slender scoreline with Radoslaw Matusiak scoring the only goal after 19 minutes to move the Poles into third place, also on 10 points. Belgium were booed off by their own fans at the end.
The top two teams in each group qualify for the finals in Austria and Switzerland in 2008.
After the winter break, the qualifiers resume in late March.
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