Opposition parties have tried to annul the vote, alleging fraud.
International observers said the election in the West African nation was marred by irregularities.
The ruling means the RPG (Rally of the Guinean People) won 53 seats, which falls short of an absolute majority in the 114-seat parliament.
“None of the complaints were supported with the necessary proof,” said Supreme Court President Mamadou Sylla.
President Alpha Conde’s main rival, Cellou Dalein Diallo, and his UFDG party won 37 seats while former PM Sidya Toure’s UFR secured 10 seats.
The remainder of seats was shared by 12 smaller parties and a period of coalition building is now expected.
A spokesman for an umbrella group of opposition parties said they were disappointed by the court’s ruling but would hold talks before announcing their next step.
The election was to replace a transitional government that has run the nation since military rule ended in 2010.
The run-up was marred by violence as well as ethnic and religious tension.
The poll was much delayed and was supposed to have been held six months after the 2010 presidential elections, which Alpha Conde narrowly won.
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