Canada's Hesjedal crossed the line in Florence after another rain-soaked stage one minute and six seconds behind a group of the race favourites to drop from sixth to eleventh place on GC.
The undulating 173km stage through the Apennine mountains from Sansepolcro to the Tuscan capital was won by Russian Belkov, who soloed to the biggest win of his career after attacking from a break on the descent of the second of four categorised climbs.
Riding his second Giro d'Italia, 28-year-old Belkov of Katusha came home 44 seconds ahead of Colombian Carlos Betancur (Ag2R-La Mondiale) with another Colombian, Jarlinson Pantano (Colombia), taking third place a further two seconds back.
"I'm so happy I won this stage, my first as a pro if we exclude the TTT," said Belkov.
"From this morning at the bus I took a look to the altimetry and I realized it was a perfect stage for my characteristics: moreover I live next to here, in Prato, so I know these roads.
"I'm thrilled I won this stage: Katusha is proving to be a really strong team here in the Giro. It's the second win, we kept the jersey for five days, and we want to continue like this in order to take some other great results.
"Yesterday I didn't do a great job, but I decided to save my legs for today, a stage dedicated to breakaways: better a first position today than a tenth place yesterday."
Sweden's Tobias Ludvigsson (Argos-Shimano) took fourth place before Australian veteran Cadel Evans (BMC) led the main pack of race favourites - including the maglia rosa Vincenzo Nibali (Astana) - over the line 1:03 in arrears.
But Hesjedal cracked on the final Cat.4 ascent of Fiesole to compound a miserable two days after his disappointing performance in Saturday's individual time trial. Last year's winner now trails Italy's Nibali by 3:11 on GC going into the race's first rest day.
It was yet another testing day for British hope Bradley Wiggins too - the 2012 Tour de France champion distanced on the wet descent of the Cat.1 Vallombrosa climb inside the final 60km.
With Astana driving a fierce pace as the rain pounded down, Wiggins dropped more than a minute off the pace and needed to be nursed back by five Sky team-mates.
Tellingly, Colombian duo Sergio Henao and Rigoberto Uran were not ordered back - perhaps a sign that Sky are prepared to consider a Plan B in the 96th edition of the Corsa Rosa as their designated leader's confidence in wet conditions continues to play into the hands of his rivals.
The seeds of Belkov's victory were sown with the formation of a 12-man break around 20km into the stage following an attack by Stefano Pirazzi (Bardiani Valvole) and Robinson Chalapud (Colombia).
Belkov, Pirazzi, Chalapud and his Colombia team-mate Pantano, Ludvigsson, Alessandro Proni (Vini Fantini), Evgeni Petrov (Saxo-Tinkoff), Michal Golas (OPQS), Giovanni Visconti (Movistar), Ricardo Mestre (Euskaltel), Juan Manuel Garate (Blanco) and Fabio Fellini (Androni) built up a lead of four minutes ahead of the first test of the day, the Cat.2 Passo della Consuma.
Chalapud and Pirazzi rode off ahead in pursuit of the KOM points with the pair almost coming to blows as the Italian inadvertently cut into the line of his fellow escapee to take maximum points over the summit. With the two leaders still arguing, Belkov drew level on the descent after attacking from the chasing group.
On the Cat.1 Vallombrosa climb - the biggest so far of the Giro - Chalapud attacked and was soon joined by Pirazzi. The pair exchanged more words and even came to a near standstill on a sodden climb through the trees as Belkov slowly returned on to their wheels.
Belkov was then allowed to ride clear as Pirazzi and Chalapud continued their bizarre spat with a bit of gamesmanship. Pirazzi soon came to his senses and put in an attack. The pair soon passed Belkov and it was the Italian who took the points going over the summit to secure the blue mountains jersey.
Although crossing the summit 47 seconds in arrears, Belkov showed his prowess on wet downhill riding by catching the leading duo with consummate ease before opening up a commanding lead off the front.
The peloton trailed at more than six minutes - and while the wet weather did not cause Wiggins to crash as he did in Friday's stage seven, the Briton quickly lost touch as Astana drove a fierce pace on the long downhill.
With Wiggins on the ropes, BMC, Garmin and Movistar all came to the front to help Astana ahead of the final two climbs of the day.
Wiggins managed to regain contact with the main pack for the Cat.3 Vetta le Croci with 25km remaining. Riding with gusto, Belkov crossed the summit two minutes ahead of Pantano and Pirazzi. The gap was reduced to just 1:20 by the time the Russian completed the final climb of the day.
But the 11% maximum gradient of the Cat.4 Fiesole - which will feature in reverse order for the 2013 World Championship Road Race in Tuscany - proved too much for Hesjedal who was quickly tailed off the back of the pursuing main pack.
With the remnants of the initial break being caught in drips and drabs, Betancur attacked from the pack in pursuit of compatriot Pantano and Ludvigsson.
Belkov held on to take his first win of the season - although this piece of information must not have reached Betancur, who outsprinted Pantano for second place before unleashing the kind of celebration reserved for maiden Grand Tour stage winners.
Once again, 2011 Tour de France champion Evans finished strongly to consolidate his second place on GC, 29 seconds behind Nibali. The Australian picked up enough points for his fifth place in Florence to move into the red jersey as leader of the points classification.
Robert Gesink (Blanco) finished in the main group to stay third, 1:15 down and one second ahead of fourth-place Wiggins, who will be praying for better weather during the all-important mountainous second phase of the race.
Michele Scarponi (Lampre-Merida) completes the top five 1:24 off the summit while, following Hesjedal's plummet down the standings, Henao rises to sixth at 2:11.
After Monday's rest day the Giro d'Italia continues on Tuesday with the first proper mountain stage of the race - a 168km ride from Cordenons to the summit of the Cat.1 Altopiano del Montasio.