The Italian clocked the time of 4:04.252 in qualifying, later defeating the UK's John Archibald for the gold medal in 4:02.647.
Just hours before, eventual bronze medallist American Ashton Lambie held the record of 4:05.423 set at altitude in Bolivia in September.
There, the American smashed his own time set in August 2018 of 4:07.251 in Mexico.
Ganna's times today in Minsk are the first world records set at sea level since Jack Bobridge sped around the track in Sydney in 2011 to post 4:10.534.
Sub-four minutes for the individual pursuit can't be too far away.
23-year-old Ganna is no stranger to racing against the clock, posting impressive performances since 2013 on the road and the track.
He is a three-time individual pursuit world champion, picking up the rainbow jersey earlier this year and in 2018 and 2016.
At the 2019 Road World Championships, he finished third behind Rohan Dennis and Remco Evenepoel in the ITT.
In Ganna's first year riding for Ineos in 2019 after a stint at UAE, he won the ITT at the Binck Bank Tour, the Italian national championships and the Tour de al Provence earlier this season.