Ellemann-Jensen, who takes over from two-time prime minister Lars Løkke Rasmussen, ran unopposed as party members selected their new leadership.
Meanwhile, former immigration minister Inger Støjberg won convincingly in a head-to-head against Ellen Trane Nørby for the deputy leader position.
“A thousand thanks for your votes and for the confidence you have shown in me. I will do all I can to live up to it,” Ellemann-Jensen said to the around 850 Liberal congress delegates after being confirmed as leader.
A former environment and food minister and political spokesperson, Ellemann-Jensen follows in the footsteps of his father, Uffe Ellemann-Jensen, who led the Liberals from 1984 to 1998.
Støjberg took 577 delegate votes to Nørby’s 206.
The two were broadly seen as representing different factions of the party, with Støjberg, an immigration hardliner, further to the right, and Nørby associated with a centrist approach considered more similar to that of Ellemann-Jensen.
“I think this is good for the Liberal party. There is now a clear mandate from delegates, so for me it is now all about treating that with humility and responsibility,” new deputy leader Støjberg said to Ritzau.
“I think most of all this should be seen as us now being a united Liberal party and that we now all want to work in tandem,” she also said.
The congress came after Rasmussen and former deputy leader Kristian Jensen announced their resignations last month.
The pair had been the two most senior members of the party, which is the largest on Denmark's right, since 2009.