But Walter-Borjans managed to tap the dissatisfaction of many Social Democrats who feel their party has abandoned its working-class origins and should abandon an alliance with conservatives.
The duo's SPD rivals, Finance Minister Olaf Scholz and Klara Geywitz, from eastern Germany, won about 45%.
In addition, a survey of SPD members by Mannheim-based pollsters Forschungsgruppe Wahlen and published on Friday by public broadcaster ZDF before the ballot was announced showed Scholz and Geywitz ahead with 38% support.
They want to renegotiate the coalition deal to focus more on social justice, investment and climate policies. The party chose to ask its 426,000-strong membership who should take on the task of pulling it out of a lengthy poll slump.
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The new leaders aren't household names to many Germans.
The victory of Walter-Borjans and Esken, who favour taxing the rich, boosting welfare spending and abandoning Germany's long-standing policy of a balanced budget, will certainly weaken pro-government forces.
Both Mr Walter-Borjans and Ms Esken have been highly critical of the German Chancellor in the past. SPD delegates will approve the leadership, chosen by a vote of the party that ended on Saturday, at a party conference that will begin on December 6.
"We didn't let ourselves be nailed down to the question of everything coming down to the question of fleeing (the coalition) or staying in permanently", Mr Walter-Borjans said. For the CDU it is quite clear: we support this coalition.
"Should the CDU not move on these important issues, we'll recommend the party make an orderly retreat", she told Bild newspaper last weekend.
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Forensic officers attend the scene in central London , Saturday, Nov. 30, 2019, after an attack on London Bridge on Friday. While condemning the attack, White House spokesperson Judd Deere offered "full support to our ally, the United Kingdom".
The Secretary General of the CDU, Paul Ziemiak, also emphasized that "nothing has changed, quot; in terms of the coalition agreement between both parties. We support this coalition on the basis of what has been negotiated".
The Social Democrats have provided three of Germany's eight post-World War II chancellors but have served as junior partners in three of Merkel's four governments since 2005.
The coalition between Angela Merkel's Christian Democrats and the SPD was formed past year.
Polls now show support for the Social Democrats at 13 or 14%.
The SPD has also been battered by a series of regional and European election setbacks this year.
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On verra qui joue avec Ben Yedder devant (.) Nous devons être attentifs en défense pour nous créer des occasions. Une chose est sure, les Parisiens devront faire beaucoup mieux face à l'AS Monaco ce soir, pour se rassurer.
Many within the party however remained wary of continuing to govern in Merkel's shadow, and the coalition has lurched from crisis to crisis. The next election is now due in the fall of 2021 but there have always been questions over whether the coalition will last until then.