Mr Laschet, premier of North Rhine-Westphalia state, defeated two rivals in the party's virtual conference.
He is now in a good position in the race to succeed Mrs Merkel when she steps down as German chancellor in September, after 16 years in office.
But he faces a changed political landscape following the Covid pandemic.
Mr Laschet, 59, defeated conservative businessman Friedrich Merz in a run-off vote by 521 votes to 466. A third candidate, Norbert Röttgen, was eliminated in the previous round.
