The 41-year old playboy-turned-politician takes over as head of state from his father, Haydar, in the first dynastic succession in a former Soviet republic.
Election official Azer Sariyev said on Thursday the majority of electors voted for Aliyev junior, and there would be no second round.
Aliyev was virtually assured of victory last night after he gained more than 50% of the votes cast, the threshold needed to guarantee a first-round victory.
With 87.5% of votes counted by Thursday morning, he had a 79.5% share of the vote while his nearest rival, opposition leader, Isa Gambar, trailed behind on 12.4%.
However, the elections have been dogged by controversy.
Aliyev's victory is being hotly disputed by his opposition opponent Gambar, who claims he is the rightful winner.
A demonstration by Gambar supporters outside his campaign headquarters in Baku turned violent on Wednesday night when riot police wielding truncheons rushed the gathering.
An AFP reporter at the scene saw dozens of people bludgeoned by police, with many bleeding from head wounds and at least two protesters knocked unconscious and dragged away by police.
Some protesters were carrying wooden clubs and metal bars and were taunting police, but the demonstration was otherwise peaceful.
Haydar Aliyev is seriously ill in an
Speaking to reporters inside his headquarters, Gambar remained defiant. "We do not intend to reconcile ourselves to the fact that the Aliyev regime has once again stolen our votes," he said.
"We will fight against that. I am the winner and I do not intend to go along with this theft."
Foreign observers are due to give thier official verdict later on Thursday on whether the elections were democratic, although they have already reported some cases of malpractice and ballot-stuffing.
Human Rights Watch, a rights organisation, has already spoken of a pre-election period during which the government manipulated election procedures and violently repressed the opposition.
Azerbaijan's presidential elections cannot be considered free and fair because of widespread abuse and bias favouring government candidates, Human Rights Watch said on Monday.
Fraud and abuse
"Azerbaijan has a sorry history of election fraud and abuse, and the current presidential election is shaping up to be more of the same," said Peter Bouckaert, senior researcher for Human Rights Watch.
However, Azerbaijan's election chiefs said the poll had been free and fair.
And the US State Department said early indications were that the voting had gone smoothly, but it added it was reserving its final judgement.
"We do not intend to reconcile ourselves to the fact that the Aliyev regime has once again stolen our votes... I am the winner and I do not intend to go along with this theft"
Azeri opposition leader
Azerbaijan's leader-to-be is a former oil executive, with little experience of politics who was thrust into the limelight when his father was incapacitated by a heart condition.
He will take charge of a republic with substantial oil reserves deep under the Caspian Sea and where western oil majors have invested billions of dollars.
Aliyev must also try to resolve an armed conflict with neighbour Armenia over the enclave of Nagorno-Karabakh which has been festering for more than a decade.
Haydar Aliyev, who is thought to be seriously ill in a US clinic, has towered over life in the country since 1969, when he was appointed Communist Party boss of the then Soviet republic.
Aliyev senior, 80, was viewed by Western companies as the figure who preserved order and opened doors to investors, hungry to tap crude oil and gas riches.
But Ilham Aliyev, many observers say, is a pale shadow of his father. He is still dogged by a youthful reputation as someone who prefers casinos and parties to affairs of state.