Henrique Rosa, who was appointed by military officers who grabbed power in a bloodless coup in the west African country on September 14, was sworn in during a ceremony in a hotel here.
The National Transition Council, which will bring together political representatives in a quasi-parliamentary role until a general election is held, was also formally set in place.
The Council is presided over by general Verissimo Seabra Correia, the armed forces chief of staff and the man who led the coup. It has 56 members, of which 25 are members of the so-called "military committee" set up by the junta after the coup, 23 party representatives and eight from civil society.
Correia said during the ceremony on Sunday that the consensus over the choice of Rosa as president was a sign of his honesty.
"This honesty will be required throughout the duration of your mandate," he said.
"The task awaiting you will not be easy, but you can count on our support," he added.
For his part Rosa said he would work for unity and would try to restore confidence between Guinea-Bissau and the international community.
And he called on the National Transition Council "to respect the dates fixed for legislative and presidential elections".
Earlier Guinea-Bissau's political leaders signed a "transition pact" designed to help steer the troubled west African country back to democracy.
All but one of the country's political parties and groupings signed the pact hammered out with the ruling "military committee".
Of the country's 17 parties and groupings, only the United Social and Democratic Party of former Prime Minister Francesco Fadul declined to sign the document.
The pact establishes the interim institutions that will govern Guinea-Bissau before it returns to democracy in two years' time.
The country's former sole authorised party, the African Party for the Independence of Guinea-Bissau and Cape Verde (PAIGC), said it would not join the transition government but would sit on the National Transition Council.
According to a copy of the pact seen by AFP, no political leader is allowed to join the transition government.
Henrique Rosa is a former head of the national electoral commission who has close links to the Roman Catholic Church.
The putschists also named Antonio Artur Sanha, the head of the ruling Party of Renewal (PRS) and an outspoken critic of the ousted president Kumba Yala, as prime minister of the former Portuguese colony. – Sapa-AFP.
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