Mr Kononenko broke the record at 0830 GMT (7:30pm AEDT), Roscosmos said.
He is expected to reach a total of 1,000 days in space on June 5, and by late September he will have clocked 1,110 days.
“I fly into space to do my favourite thing, not to set records,” Mr Kononenko told the TASS news agency in an interview from the International Space Station (ISS), where he is orbiting about 423 kilometres from Earth.
“I am proud of all my achievements, but I am more proud that the record for the total duration of human stay in space is still held by a Russian cosmonaut.”
The 59-year-old took the top spot from Mr Padalka, who had accumulated a total of 878 days, 11 hours, 29 minutes and 48 seconds, Roscosmos said.
The Soviet Union spooked the West in the early years of the space race by being the first to launch a satellite to orbit the Earth (Sputnik 1) in 1957, and then Soviet cosmonaut Yuri Gagarin became the first man to travel into space in 1961.
Top 5 Astronauts who spent the most time in Space:
1. 🇷🇺 Oleg Kononenko – (878 days 11 hours 29 minutes 48 seconds)
2. 🇷🇺 Gennady Padalka – (878 Days)
3. 🇷🇺 Yuri Malenchenko – (827 days 9 hours)
4. 🇷🇺 Sergey Krikalyov – (803 days 9 hours)
5. 🇷🇺 Alexander Kaleri – (769 days 6 hours)