Commissioned a Second Lieutenant, Bondarenko served in the Soviet Air Force's PribVO (the former Baltic Military District), and on April 28, 1960 he was chosen to be among the first group of 29 cosmonauts. He began training on May 31 for an intended launch on the spacecraft Vostok 1 (aboard which Yuri Gagarin carried out the first human spaceflight a year later).
Because of the pressure difference, it took a watching doctor nearly half an hour to open the chamber door. Bondarenko's suit burned until almost all the oxygen in the pressure chamber was used up and he had suffered third-degree burns over most of his body. The attending physician at Botkina Hospital, surgeon and traumatologist Vladimir Golyakhovsky, recalled in 1984 that while attempting to start an intravenous drip the only blood vessels he could find for inserting a needle were on the soles of Bondarenko's feet, where his flight boots had warded off the flames. According to Golyakhovsky, cosmonaut Yuri Gagarin spent several hours at the hospital as "deathwatch officer", and Bondarenko died of shock 16 hours after the mishap, less than three weeks before Gagarin's historic spaceflight. Manned orbital flight program director Nikolai Kamanin blamed Bondarenko's death on the Institute's poor organisation and control of the experiment.
Bondarenko is buried in Реликтовая липовая роща in Novosibirsk, where his parents were then living. After his death Bondarenko's wife Anya left her job at the Cosmonaut Training Centre. His only child Aleksandr also later became a fighter pilot. The Presidium of the Supreme Soviet of the USSR posthumously awarded him the Order of the Red Star on June 17, 1961.
James Oberg, in his book Red Star in Orbit, wrote how the Soviet government made an Orwellian attempt to airbrush out the cosmonaut's image from an official 1961 photograph of the first six cosmonauts selected for training, while British researcher Rex Hall showed that five people had been erased from an earlier group photograph of 16 cosmonauts. Clumsy attempts were later made to further "doctor" the historic photographs, with the insertion of imaginative but nonexistent photo details to account for the absence of the original members of the group.
The circumstances of Bondarenko's death were similar to those which befell the crew of Apollo 1. There was some later speculation that, had the Soviets been open about the Bondarenko tragedy, NASA might have been alerted to the hazardous design of the early Apollo command module and would have made changes which could have prevented the 1967 deaths of the three Apollo 1 crew members. However, by 1966 the lethal hazards of a high-pressure 100-percent-oxygen environment had been thoroughly described in American scientific publications.