In a shocking twist Wednesday, he turned up alive at a news conference and revealed he was informed a month ago about the plan to fake his death.
Details of the sting operation were not clear, including why authorities chose to go to such lengths to make it look as if Babchenko was dead.
Petro Poroshenko, Ukraine's president, tweeted praising the efforts of security services and saying the operation had to take place for the safety of Babchenko and his family as Russian Federation was unlikely to back down.
"I will congratulate his family and all of us and Arkady Babchenko on his birthday".
Russian Foreign Ministry Spokeswoman Maria Zakharova said Wednesday finding out Babchenko was still alive came as the "best news".
Mr Babchenko has also been a contributor for Russia's top opposition paper the Novaya Gazeta.
"I am sorry, but there were no options here", Babchenko said at the presser.
Gritsak said the agency had collected proof his assassination had been ordered by the Russian security services. He explained the operation was successful after Ukraine's security services arrested the suspect.
In a social media post soon after news of his death emerged, the Ukrainian Prime Minister, Vladimir Groysman, said it held Russian Federation responsible. "The operation was under preparation for two months".
"The important thing is my life has been saved and other, bigger terrorist attacks have been thwarted", he said.
After moving to Ukraine from Russian Federation in February 2017, Babchenko continued to receive death threats, but reportedly did not take them seriously, according to someone who knew him.
The 41-year-old journalist had spoken publicly about the threats against his life and the fear that drove him to leave Russian Federation.
Arkady Babchenko, who moved to the city previous year following threats in his homeland, was sacked on after returning from buying bread and died of his injuries in an ambulance, local police said late Tuesday.
Moscow's annexation of Crimea and support for separatist insurgents in eastern Ukraine were topics on which the journalist was scathingly critical of the Kremlin.
Babchenko fought in Russia's two Chechen campaigns in the 1990s and early 2000s before becoming a war correspondent and author. It was reported that his wife found him and called the ambulance. Babchenko did not take the intimidation too seriously, according to Ponomarev. The Ukrainian government treated Mr Babchenko's death as real following the staged incident.
Moscow added it hoped that Ukraine's foreign sponsors and worldwide organizations would draw the right conclusions from the story about how matters of life and death are handled by Kiev.
Authorities had received information about a Russian security services plot to kill Babchenko and managed to prevent it.