Officials said Mr Guelleh won 87% of Friday's vote, which activists complained was preceded by political repression and curbs on basic freedoms.
Mr Guelleh, in power since 1999, begins a fourth five-year term in power.
He faced five rivals in the election, but three opposition parties boycotted the poll.
The opposition complain of police brutality and media bias under Mr Guelleh's rule.
"The people of Djibouti have again entrusted me with the state's highest office," Mr Guelleh, 68, said in a speech on national TV.
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Djibouti election: What you need to know
Djiboutiâ€™s thin-skinned democracy
Djibouti's strategic position on the Gulf of Aden means that it is home to US and French military bases.
The country is also seen as relatively stable in a region which includes Somalia, where the government does not control the whole country, and Yemen, where there is a civil war.
Observers say this explains the muted criticism of President Guelleh from the West.
Some 180,000 people were eligible to vote, around a fourth of the population.
The opposition were angry that the president rescinded his earlier decision not to seek another term.
His main rival, representing the opposition Union for National Salvation (USN) coalition, was Omar Elmi Kaireh, a Djibouti independence hero.
He came second, with 7%, according to provisional results announced by Interior Minister Hassan Omar.

The sum is half the record Lotto jackpot win - shared with a couple from Hawick who claimed their prize within days of the 9 January draw.
A spokesman for organisers Camelot urged players to "check, double-check and triple-check" their tickets.
The ticket had the winning numbers 26, 27, 46, 47, 52 and 58.
Updates on this story and more from Worcestershire
Camelot said the exact location where the ticket was purchased could not be revealed but it hoped that by naming the area where the ticket was bought it could increase local interest and help find the winner.
The area has not been narrowed down further to preserve the winner's anonymity, they said.
It is not known if the winning ticket was bought by an individual or a syndicate.
David and Carol Martin, both aged 54, received a cheque for £33,035,323 after claiming their share of the record jackpot, that occurred after 14 successive rollovers.
Even though the prize total was shared, the sum is still the biggest win since the National Lottery was launched in November 1994.
However, the sum is dwarfed by the the biggest UK win in the Euromillions lottery, a draw where prize money comes from ticket sales in several European countries.
Colin and Chris Weir, from Largs in North Ayrshire, collected £161.6m in 2011.

Matthew George was held by police investigating historical allegations at Kerelaw School.
The 67 year old taught art at the school and secure unit, which closed in 2006 following a police probe into incidents of abuse.
He is expected to appear at Kilmarnock Sheriff Court later.
A report is to be sent to the procurator fiscal.
The school was originally run by Strathclyde Regional Council and its successor, Glasgow City Council.
Djibouti's President Ismail Omar Guelleh has won a landslide victory in an election criticised by opposition parties and rights groups.
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An unclaimed National Lottery jackpot winning ticket that could earn the winner £33m was bought in the Worcester area, it has been revealed.
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A former teacher has been arrested in connection with sexual and physical abuse allegations at a former residential school in Ayrshire.