There were delays in opening some polling stations and reaction to an opposition call for a boycott was mixed. Many people voted early, partly to avoid 40-Celsius heat later.
Polling stations were largely empty by early afternoon but no figures were available for the turnout among the 5 million registered voters. Results are not expected for about a week.
Deby has ruled the central African state, which produces around 115,000 barrels of oil a day, since seizing power in a 1990 coup and winning three subsequent elections.
“We have come to give our vote of confidence for Deby for all he has done for the country,” said Ahmat Saboun, who voted in the Djambal Barh neighbourhood.
“We are ignoring the opposition,” Saboun added, referring to Deby’s rivals, who have rejected the validity of the poll after the government threw out their request to revamp the voter register.
Opposition leaders Abdelkader Wadal Kamougue, Ngarledjy Yorongar and Saleh Kebzabo said thousands of unattributed voter cards from a February 13 legislative poll, won by Deby and his allies, were still in circulation and could be fraudulently used on April 25.
“We cannot possibly sanction this masquerade,” Kamougue said on Monday. Deby now faces only two minor candidates in the poll.
Some residents of the capital were also cynical. “There is no point in voting in an election whose result is known in advance in any case,” said Djibrine Ibet.
“What hope is there when the party in power refuses to print new election cards because they are afraid of losing?”
The incumbent says the opposition are boycotting the poll because they know they would lose.
Deby has spent much of the last five years since his last win in 2006 tackling a rebellion in the east. In 2008 he faced a rebel barrage of the capital that killed hundreds.
But he has since made peace with Sudan, ending what analysts said was a proxy war fought by each country’s rebels.
The World Bank helped Chad build a pipeline to export its oil as part of an agreement that was meant to see the government devote revenues to fight poverty.
But the deal collapsed when Chad spent the funds elsewhere.
Deby has signed two huge infrastructure deals with China in recent months, including a $7.5 billion agreement with China’s CCECC engineering company to build 1,344 km (835 miles) of railway.