It's the end of an era in Germany.
In recent weeks, the new party leader sought to put a careful distance between herself and Merkel without disavowing her, saying she has had "very lively discussions" with the chancellor on various subjects.
A staunch Catholic, Kramp-Karrenbauer has spoken out in favour of a ban on doctors who carry out abortions being able to advertise their services, after a court case propelled the topic into the headlines, and is also openly sceptical about the "marriage for all" law campaigned for by her opponent, Jens Spahn, who is married to his male partner.
1001 delegates are electing a successor of German Chancellor Angela Merkel who doesn't run for party chairmanship after more than 18 years at the helm of the party.
Accepting a lengthy standing ovation from delegates, many tearful and holding "Thanks, boss" placards aloft, a visibly moved Merkel said the party had won 4 national elections under her by holding fast to its principles. However, Carsten Brzeski, Chief Economist at ING Germany is less optimistic about the outcome, and doesn't see any clear way forward for the CDU in the wake of Kramp-Karrenbauer's close victory over her more conservative rival Merz. If their candidate, BlackRock Inc.'s Friedrich Merz, beats Merkel acolyte Annegret Kramp-Karrenbauer the chancellor's plans for a final three years in office may be called into question.
Her popularity has waned since her 2015 open-doors migrant policy and the CDU has suffered heavy electoral losses at the state level.
Merkel, however, recalled that the CDU was in a deep crisis when she took over in 2000, mired in a party financing scandal surrounding ex-Chancellor Helmut Kohl.
"Merz was just a bit too free-market, pro-American and pro-defense".
"Domestically, AKK is likely to sharpen the social policy profile of the CDU and she can appeal to some on the party's more conservative wing", Jorns Fleck, an expert on German politics, told Newsweek.
There was jubilation as the result of the run-off was announced.
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'I wasn't born as chancellor or as party leader, ' she said. Kramp-Karrenbauer is 56 and Merz 63, only a year younger than the chancellor. "Good luck! Now it's time to solve problems: shoring up the future of pensions, recognizing the value of work, strengthening cohesion in Europe".
Merkel, 64, has presided over Europe's most populous country and powerful economy for 13 years.
The CDU has bled support to the right in the form of the AfD, as well as to the resurgent Greens.
Earlier, an emotional Merkel bowed out as party leader, telling the congress: "It has been a great pleasure for me, it has been an honor".
Kramp-Karrenbauer, 56, has differentiated herself from Merkel on social and foreign policy by voting in favour of quotas for women on corporate boards and by taking a tougher line on Russian Federation.
Kramp-Karrenbauer says she knows how to win elections, having defied expectations to win re-election in Saarland by a wide margin previous year.
That practical, non-ideological approach is similar to the style Merkel has employed as chancellor.
"We are in demanding times today, no doubt about that", she said.
"Schaeuble's manoeuvre shows: the CDU of the old Germany is trying to make a comeback", news weekly Der Spiegel said.