Italian Stefano Pirazzi (Bardiani-CSF) held off a small group of chasers in the home straight to claim his maiden Giro d'Italia victory in the 17th stage on Wednesday.
Race leader Nairo Quintana (Movistar) crossed the finish line with the main peloton and his closest rivals nearly 15 minutes later following a 208km trek from Sarnonico to Vittorio Veneto that saw a breakaway go unchallenged all the way to the finish.
Quintana, the runner-up on last year's Tour de France, spent his first day in the race's fabled 'maglia rosa' (pink jersey) to retain his 1min 41sec lead on Rigoberto Uran (Omega-Pharma) and 3:21 cushion on Australian Cadel Evans (BMC).
But it was a tense day in the saddle for the 24-year-old Colombian, who was accused of foul play following his victory on stage 16 when he took the jersey from Uran, last year's runner-up, and then faced calls for his time advantage to be cancelled.
Quintana said of Tuesday's controversy: "We're making a story out of nothing. Why should they take a time advantage away that I earned out on the road?
"I don't understand the problem. Most of the time I made, I did on the final climb."
Uran's Omega-Pharma team were on Tuesday among several to accuse organisers, and Quintana, of foul play following an official radio announcement during the rain-plagued 16th stage that suggested the descent of the treacherous Stelvio climb would be 'neutralised' -- effectively not raced -- because of the dangers posed by cold and wet conditions.
Organisers later claimed they had simply announced that a motorbike rider, with a pillion passenger waving a red flag, would be placed at the front of the race to warn of any dangers on the road ahead.
As some teams and riders heeded the organisers' 'advice', others, like Quintana, forged on ahead regardless. Quintana claimed the win, the pink jersey and put himself in contention for a first Grand Tour triumph four days before the finish.
"The results should have been cancelled," said the owner of Tinkoff, Oleg Tinkoff, whose team leader Rafal Majka dropped to 3:28 behind Quintana on Tuesday.
Two meetings between several unhappy cycling teams were held, while the International Cycling Union (UCI) attempted to defuse the situation by tweeting that the organisers had "taken the initiative by putting motorbike riders ahead of the peloton" and that "security remains the main concern of all race organisers and the UCI."
With moods tense, there was little reaction from the main bunch when an early breakaway formed and went on to build a healthy lead that stood at 12 minutes with a little over 50km remaining.
After a series of attacks and counter-attacks in the closing kilometres, Pirazzi broke free in the final 1.3km and just thwarted a small chasing group from ending his bid metres before the line.
His first Giro win was celebrated by a defiant gesture at the finish, after which Pirazzi explained: "It's my response to all my critics."
"I've been searching five years for this victory, it was beginning to get me down, but finally I've done it," added the 27-year-old.
"A lot of people criticised my lack of results, but I can assure them I've been working hard. This is my reward for that."
It was also Bardiani-CSF's third win inside a week, following successes by Marco Canola and Enrico Battaglin on the 13th and 14th stages.
On Thursday the race moves back into the mountains on the 18th stage from Belluno to Panarotta Refuge.
Two mountain passes, the San Pellegrino and the Redebus, will be crossed before the peloton tackle the 16.8km rise to the finish.