Businessman Malik Saidullayev said on Thursday the Chechen supreme court ruling was inspired by Kremlin officials who want to ensure victory for Akhmad Kadyrov.
A former grand mufti of Chechnya, Kadyrov was appointed by Russia to run the pro-Moscow administration in the North Caucasus republic three years ago.
Saidullayev said: "We will appeal to the Russian Supreme Court in the next few days. We will get the explanation for the ruling tomorrow."
The main opponent to Kadyrov, Saidullayev was the only serious alternative in the presidential race after the withdrawal of three other contenders.
One of these, Aslanbek Aslakhanov, Chechnya's lone deputy in Russia's lower house of parliament, announced he was quitting the race only a few hours earlier.
Kadyrov was also indirectly accused by Saidullayev of using murder and kidnapping to intimidate his supporters.
The candidate's team said armed people with portraits of Kadyrov pinned to their breasts had shot dead on Tuesday the son of one of Saidullayev's main election campaigners.
And on Wednesday, another campaign activist of Saidullayev was abducted by gun-toting men in the village of Sernovodskaya, the campaign headquarters said.
Russia launched its second war
on Chechnya in a decade in 1999
An opinion survey released this week showed the vast majority of Chechens did not believe the elections would be free and fair.
Tuesday's poll said 68% of Chechens did not have faith in the elections and 51% thought Kadyrov would win no matter what.
The October 5 election is a showpiece in the Kremlin's efforts to convince the Russian people and the world that the war in the Caucasus is over.
But critics have said it is impossible to hold a legitimate election in Chechnya, which has been shattered by the years of war and where soldiers, rebels and civilians die nearly on a daily basis.
The war has slowly bled the Russian forces of its men - official estimates say about 5000 soldiers have been killed in the conflict, while rights groups estimate the number to be around 12,000.
Tens of thousands of civilians are also believed to have died since the start of the conflict in October 1999, the second war between separatists and Russian troops in a decade.