Mr Conde, 77, won with about 58% of votes cast.
The main opposition leader, Cellou Dalein Diallo, has called for peaceful protests against the outcome. Guinea’s voters were the victims of an electoral hold-up, he said.
Election observers said the vote was valid despite some logistical problems.
Candidates now have eight days to file complaints before the constitutional court validates the results.
However Mr Diallo said in a statement he would not appeal to the court. He pulled out of the elections on Wednesday alleging fraud.
The allegations included ballot boxes being stuffed and some 400 polling stations staying closed.
It was Guinea’s second democratic presidential election since independence from France in 1958.
Clashes during the election campaign claimed several lives.
Mr Conde became president in 2010 in the country’s first democratic election after decades of fighting authoritarian regimes, during which he was sent into exile and prison.
He defeated Mr Diallo in a run-off.