The Colombian was in a podium position in this year's Tour de France, leading Ineos Grenadiers' overall classification challenge, when he struggled on the stage to Grand Colombier and lost over seven minutes. The next day, he gave up even more and then dropped out of the race in the third week.
While visiting the Vuelta a Colombia on Saturday, Bernal told Signal Colombia television that he has always had back problems.
"The pain is really something very old, last year during the Tour that I won, the first year that I raced the Tour and since when raced mountain bikes, I've always had a pain there," he said.
Last month, Bernal told ESPN Colombia, "The problem is that one leg is longer than the other... It's a pretty long recovery process because basically it has caused me to have scoliosis in my spine."
He speculated that the pain is coming from a pinched nerve in his spine that runs down into his leg and a too-rapid ramp up to the second part of the season caused it to flare up.
Bernal began the second part of the season after the coronavirus break with a victory in La Route de Occitanie and second place in the Tour de l'Ain but struggled in the Critérium du Dauphiné with pain in his back.
"During the quarantine, with so many hours on the rollers and then going from zero to the intensity of the races in France before the Tour, I think that made a pinched nerve in the vertebra a bit irritated and that's where the pain is coming from," he said on Saturday.
"I feel fine, it is a bit of a complicated injury, but we are working very hard to be able to be at the level that I should be next year.
He said he has a "whole team of doctors" monitoring his progress and testing to locate the source of the pain.
Today's best Black Friday deals
Today's cycling-related highlights from the Black Friday sales. For even more, view our guide to the best Black Friday bike deals where you'll find on all things cycling, including bikes, helmets, clothing and more.
Today's best deals: USA
Jenson USA: 25% off Shimano RC902 shoes
Competitive Cyclist: 60% off Assos S.J.Blitzfeder rain jacket
Chain Reaction Cycles: LifeLine 18-piece tool kit
$73.99| $49.99 | 32% off
Today's best deals: UK
ProBikeKit: 300-lumen rear Lezyne light for under £35.00
Chain Reaction Cycles: Endura MTR Shell Jacket
£139.99| £76.99 | 45% off
Rutland Cycling: 36% off Moon Storm & Nebula lightset