Kern, who stepped down as head of the opposition Social Democrat (SPOe) party last month, earlier indicated he had considered putting himself forward as a candidate to take over from Juncker.
But on Saturday, the 52-year-old told reporters he was ending his career because "domestic political games" were overshadowing key debates over European parliamentary elections in May 2019.
"As a former head of government, it's impossible to leave the domestic political stage," he said in Vienna.
Describing next year's parliamentary vote as "the battle of all battles over the future of our continent", Kern said Europeans had to unite to avoid a takeover by far-right and rightwing parties.
Kern became chancellor in 2016, but lost in a snap election to conservative Sebastian Kurz just a year later.
At an EU summit in Salzburg last month, he had sought to drum up support for his candidacy for the EU's most powerful job ahead of a meeting in Lisbon in December where the Social Democrat (S&D) grouping will choose its contenders.
Juncker is scheduled to leave office at the end of October 2019 after a term marked by a series of crises, including a huge influx of refugees, soaring debt and Brexit.
His successor will be chosen by a so-called "Spitzenkandidat" procedure, a term meaning "lead candidate" in German, which was used was for the first time to appoint Juncker in 2014. Under the system, the largest party in the European Parliament after elections nominates its contenders for the post.
Commission vice president Maros Sefcovic, a 52-year-old Slovakian, has already announced his candidacy for the S&D grouping. It is the second biggest group in the European Parliament after the right and centre-right EPP from whose ranks Juncker came.
The German head of the EPP parliamentary group, Max Weber, enjoys the support of German Chancellor Angela Merkel and is seen as a frontrunner.
Last week, former Finnish prime minister Alexander Stubb also threw his hat into the ring for the EPP grouping.