Conte eclipsed a little-known challenger in a vote which was snubbed by main opposition parties.
State media said on Wednesday that Conte had won 95.63 % of the votes from a turnout of 82.76%, leaving rival Mamadou Bhoye Barry with just 4.37%.
The president has ruled the former West African French colony with an iron fist since seizing power in a 1984 coup.
He was widely expected to win as opposition parties boycotted Sunday's vote, saying it would not be fair. They soon denounced the result.
"This is foolishness... from now on we no longer recognise this rule"
Opposition coalition spokesman
"This is foolishness... from now on we no longer recognise this rule," Mamadou Ba, a veteran politician and spokesman for the main opposition coalition, said.
The result, which needs to be rubber-stamped by the Supreme Court, paves the way for Conte to rule until 2010 even though his poor health has raised fears of instability in the country.
The vote focused attention on the president's failing health. A diabetic chain-smoker, Conte has rarely appeared in public over the past year and has repeatedly undergone medical treatment abroad.
He stayed in his four-wheel drive vehicle to vote on Sunday, handing his ballot to an aide to put in the urn.
Opposition leaders have previously urged the army to seize power temporarily in Guinea, which has a third of the world's bauxite reserves.
It also borders Sierra Leone, Liberia and Ivory Coast - all casualties of civil war in recent years.
Earlier on Wednesday, Barry claimed a surprise victory saying that according to his observers in polling centres he had snapped up 56% of the votes.
He said he he would not recognise the official tally if Conte won, but declined immediate comment after the official results were announced.
But a spokesman for the ministry of territorial administration dismissed Barry's victory claim, saying he had excluded himself from the democratic process by giving his own figures.
Guinea has an undistinguished record on holding election polls.
Mamadou Bhoye Barry (L) was
the only challenger
In June this year, long-delayed legislative elections were held and the ruling party won more than a two-thirds majority in the National Assembly.
The European Union refused to fund or monitor the elections as irregularities were feared.
Twelve political parties participated, but afterwards some claimed the elections had been rigged and that voters had been intimidated by government officials.
A day after the election results were announced, President Conte banned all street demonstrations.