The day of voting, which ran from 7:00 am to 6:00 pm (0600 GMT to 1700 GMT), ended without incident despite rebel threats to upset the process.
No turnout figures were immediately available, but participation by the country's 5.8 million eligible voters appeared low, with few people gathering at polling stations in the capital, AFP journalists witnessed.
Observers reported seeing more soldiers than voters at polling stations in the capital, N'Djamena.
Deby is set to win a third term after the main opposition parties said they were boycotting the election.
"All Chadians have come out to make their choice, the choice of their convictions," said Deby after casting his own vote.
"This is enough proof that the people of Chad are mature. They don't need anybody to tell them to boycott elections."
Turnout appeared low as voters trickled to improvised polling stations. At some polling stations, election officials appeared to be helping voters in their choice.
"You vote for the president. You put his slip into the envelope and put it into the ballot box," a female election official told one voter.
The poll comes just three weeks after rebel groups laid siege to the capital but failed to over-run it.
That attack was defeated by government troops, and Chad cut diplomatic relations with Sudan after Deby accused Khartoum of supporting the rebels.
"These elections do not interest us. We know who will win," said student Masra Pall in a market in a poor eastern area of the capital where many people heeded the opposition call.
Deby seized power in 1990, but won elections in 1996 and 2001 that critics say were neither free nor fair.
Supporters of the president rally
in N'Djamena on Wednesday
In 2005, he won a national referendum to change the constitution allowing him to stand for a third term after opposition parties boycotted the vote.
His supporters say he offers a guarantee of stability in the face of conflict on the country's eastern borders in the Darfur region of Sudan.
Critics say Deby has built a government based on clans and corruption and that he is siphoning off oil profits earmarked for development.