Two of the expected four favourites for the title struggled, with Vuelta a Espana champion Primoz Roglic exhausted from his exploits earlier this month and finishing three minutes down in 12th, while Belgian specialist Victor Campenaerts crashed, and later needed a bike change, and was only 10 seconds better than Roglic in 11th.
Bevin, meanwhile, paced his ride smoothly. He was in ninth place through 16.7 kilometres of the 54 kilometre course, before moving into sixth through 37.7 kilometres.
In the final period of the testing course, his times saw him pass Portugal's Nelson Oliveira and Estonia's Tanel Kangert, but having been just 1.29 seconds behind Ganna at the penultimate checkpoint, he couldn't claw back the miniscule margins to claim what would have been a historic medal.
"It's a big step forward. That's two worlds in a row where I've turned up and performed," Bevin said.
"It was an improvement but it's pretty disappointing to miss the podium by such a small amount. That being said you kind of go back to the drawing board and you always want a bit more."
The 28-year-old claimed a bronze last year in the now-defunct trade team time trial, and while New Zealanders have won medals in the junior and under 23 levels of the world championships, no male has ever claimed an individual medal at the highest level of the world's pinnacle event.
Bevin's efforts in the time trial last year - where he finished eighth - was previously New Zealand's best finish in the race against the clock, and while he and three Kiwi teammates will have a chance in the road race to bring home a medal on Monday, today was New Zealand's best chance of creating history.
It wasn't to be, and while the excellent effort confirms Bevin as a medal chance at the Tokyo Olympics, those two seconds may remain a cruel reminder of how he came so close.