His victory means that the Déby family’s 34-year-rule will continue.
After the results were announced, supporters of the ruling coalition stormed the streets of N’Djamena to celebrate Gen Déby’s victory.
In his victory speech posted on social media, he promised to serve all Chadians – “those who voted for me and president for those who made other choices”.
“I have a special thought for the unfortunate candidates who have lost the competition.”
Just before the election results were announced, Prime Minister Masra claimed victory in a live broadcast on Facebook, and called on his supporters and security forces to oppose what he said was an attempt by Gen Déby to “steal the victory from the people”.
“A small number of individuals believe they can make people believe that the election was won by the same system that has been ruling Chad for decades,” he said.
“To all Chadians who voted for change, who voted for me, I say: mobilise. Do it calmly, with a spirit of peace,” he added.
The results of Monday’s election were announced two weeks earlier than expected.
They still have to be confirmed by the Constitutional Council.
Chad becomes the first of the countries where the military seized power in West and Central Africa in recent years to hold elections and restore civilian rule.
But critics say with the election of Gen Déby, little has changed.
Monday’s voting was mostly peaceful but at least one voter was killed, according to local media.
There had also been some opposition reports of irregularities on polling day.
Ten politicians who had been hoping to run were excluded by the constitutional council because of “irregularities”, which some say was politically motivated.
Another potential opponent, and a cousin of Gen Déby, Yaya Dillo, was killed by security forces in February while allegedly leading an attack on the National Security Agency in the capital, N’Djamena.
Activists had called for a boycott of the election.
Many are still in exile following a deadly crackdown on opponents following protests in October 2022.
The oil-exporting country of nearly 18 million people has not had a free-and-fair transfer of power since independence from France in 1960.
Idriss Déby overthrew Hissène Habré in 1990 and remained in charge for the following three decades until his battlefield death in April 2021 at the age of 68.
Gen Déby initially pledged to stay as interim leader for just 18 months, a period that was later extended. He also said that he would not run for president.