Ottmar Hitzfeld's team failed to score for the first time in their Group Two campaign, against an Israel side who played with 10 men for the final half-hour after Avihai Yadin was sent off.
Eren Derdiyok went closest for the hosts with a free header which bounced up and over Dudu Aouate's goal, but the lack of goals did not prove costly as the point enabled them to top the group.
Greece, the group runners-up, will be in the draw for the play-offs after they beat Luxembourg 2-1 in Athens.
Vasilis Torosidis headed the Greeks in front on the half-hour mark and Theofanis Gekas, scorer of four goals in Saturday's 5-2 win over Latvia, added a second goal three minutes later.
Ben Payal was dismissed for the visitors in the 58th minute after being shown a second yellow card, to reflect a miserable night and qualifying campaign for Guy Hellers' team, whose only consolation came in the last minute when Avraam Papadopoulos turned a cross past his own goalkeeper Michalis Sifakis.
Greece failed to add to the score but sealed a result which sees Otto Rehhagel's 2004 European champions clinch their place in Monday's play-off draw where they will be one of the seeded teams.
Latvia leapfrogged Israel into third place by beating Moldova 3-2 in the other game in the group.
Gheorgi Ovseannicov gave Moldova, the group's bottom side, a 25th-minute lead but Latvia led by half-time thanks to a double from Andrejs Rubins (31 and 44).
Kristaps Grebis added a third goal for the Latvians seven minutes after his 69th-minute introduction as a substitute.
Veaceslav Sofroni pulled one back for Moldova with a minute to go but they could not find an equaliser.