Merkel, 59, will have a four-year term after being overwhelmingly elected by 462 votes in the Bundestag, the lower house of parliament, where her new left-right coalition holds a comfortable majority.
"I accept the election result and thank you for your trust," said Merkel after the confirmation vote in the Bundestag. Smiling, she received a bouquet of flowers and shook hands with other MPs.
Merkel's conservatives secured a stunning hat-trick win with 41.5 per cent of the vote in the September 22 elections but failed to grab an outright majority, forcing her to enter into lengthy coalition negotiations with initially reluctant centre-left Social Democratic Party.
Germany's first female chancellor held talks with rival SPD lawmakers, who voted on Sunday to back the 'grand coalition' after her previous junior coalition partners, the Free Democrats, for the first time failed to win any seats in the elections.
Merkel's centre-right Christian Democrats Union bloc and the SPD now command a huge majority in the Bundestag with a whopping 504 of the 631 seats.
For today's vote, 621 members of parliament were present, of whom 150 voted against Merkel, with nine abstentions.
Lawmakers began the vote by standing for a short memorial to South African peace icon Nelson Mandela who died this month, as Bundestag president Norbert Lammert paid tribute to his example in fighting racism.
Merkel went to the palace of President Joachim Gauck to be confirmed in the post and returned to the Bundestag to be formally sworn in as Germany's only third post-war chancellor to win a third four-year term after her mentor Helmut Kohl (1982-1998) and Konrad Adenauer (1949-1963).
Raising her right hand, Merkel took the oath of office and received a standing ovation from lawmakers before taking the first seat on the new government bench.
The new cabinet will meet for the first time after Merkel's ministers are sworn in, bringing the chancellor back to business in the EU's most industrialised state.
Germany's tough stance on fiscal discipline is unlikely to change under the new coalition.
The new government will be slightly to the left of the previous one, in which the CDU were in coalition with the market-oriented Free Democrats, BBC reported.
But the SPD will form a minority part of the government and no one doubts that Merkel will be in charge.
As the EU's most populous state, with its biggest economy, Germany dominates decision-making for the eurozone.
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