An emotional Mr Babchenko, who has been a critic of Russian President Vladikir Putin, thanked the Ukrainian security service for saving his life.
Before ushering Babchenko into the room, Gritsak said the Ukrainian allegedly recruited by Russian agents to kill the reporter had hired an acquaintance to be the gunman.
The freakish scenes were a shock to everyone - including Mr Babchenko's wife, who received an apology from her husband for faking his own death. He left Russian Federation in February 2017, writing that it was "a country I no longer feel safe in".
Babchenko served as a soldier in both wars in Chechnya before turning his bleak experience into the acclaimed memoir One Soldier's War.
On Wednesday Russian foreign ministry spokeswoman Maria Zakharova said the affair was a propaganda exercise by Ukraine, but that she was happy Babchenko was alive.More news: FBI Issues Warning After Russia Malware Attacks: 'Reboot Your Routers'
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"I am sorry, but there were no options here", Babchenko said at a news conference.
The prominent 41-year-old journalist was reported to have been shot dead in the stairwell of his apartment building in Kiev in an apparent assassination.
Babchenko, 41, fled his native Russia for Ukraine a year ago after receiving death threats for criticizing Russian military involvement in Syria.
He had previously been scathingly critical of Moscow's policies, assailing its annexation of Crimea, its support for separatist insurgents in eastern Ukraine and the Russian campaign in Syria.
According to the Moscow-based independent newspaper Novaya Gazeta, where he had worked until 2011 as a war correspondent, Babchenko was shot in the back in the entrance of his Kiev home by an unknown assailant or assailants. The final straw, he wrote in a Facebook post later reprinted by the Guardian, came just a few months before he fled, following his December 2016 post after the crash of a Russian military plane in the Black Sea.
One day later, he appeared at a news conference in Kiev.