The Slovakian youngster from Liquigas outsprinted Germany’s Andre Greipel (Lotto Belisol) and Australian Matt Goss (Orica GreenEdge) to secure a historic hat-trick in his debut Tour.
But the race was thrown into chaos once again after a mass pile-up saw the likes of Frank Schleck (RadioShack), Janez Brajkovic (Astana), Michele Scarponi (Lampre), Robert Gesink (Rabobank) and Alejandro Valverde (Movistar) lose more than two minutes in the overall standings.
Giro d’Italia winner Ryder Hesjedal (Garmin-Sharp) crossed the line more than 13 minutes down on Sagan while France’s Thomas Voeckler (Europcar) lost more than six minutes. Britain’s Mark Cavendish (Team Sky) was also caught up in the crash, meaning the world champion could not compete for the spoils.
Switzerland’s Fabian Cancellara (RadioShack) finished safely inside the main group alongside race favourites Cadel Evans (BMC) and Bradley Wiggins (Team Sky) to retain his yellow jersey.
The 208km stage was turned on its head by the accident, which occured on a long downhill drag on the road to Metz as the peloton chased down a four-man break that had jumped clear moments after the start at Epernay, the Champagne capital of France.
The break was instigated by American David Zabriskie (Garmin-Sharp), who alongside Davide Malacarne (Europcar), Romain Zingle (Cofidis) and Karsten Kroon (Saxo Bank-Tinkoff) built up a maximum lead of just under seven minutes under stormy skies in northern France.
That lead had been reduced to under one minute when the stage’s decisive moment occured. A touch of wheels near the front of the peloton caused a massive pile-up and affected over half the field.
The crash altered the dymanic of what had seemed like a rather routine final flat stage ahead of the medium mountains over the weekend.
Greipel, who had been involved in two smaller incidents earlier in the stage, found a second wind – and despite telling his team-mates he would sit out the expected sprint in Metz, had a change of mind.
With his Lotto Belisol train largely intact following the crash, Greipel was the overwhelming favourite to secure a third successive victory on the Tour.
But Tasmanian sprinter Goss was also well placed within the main group and surrounded by a number of capable GreenEdge team-mates.
The leading quartet were caught with just two kilometres to spare, Zabriskie the last to throw in the towel. Greipel was once again led out expertly by Greg Henderson, holding off the challange by Goss but underestimating a late surge of place from the indefatigable Sagan.
Coming from behind and without the aid of a lead-out, the 22-year-old green jersey roared past both Goss and Greipel to take his third win of a superb debut Tour – unveiling a new celebration, The Indredible Hulk, as he crossed the line.
Greipel was beaten by a bike length into second, with Goss taking third ahead of Dutchman Kenny van Hummel (Vacansoleil-DCM) and Argentina’s Juan Jose Haedo (Saxo Bank-Tinkoff).
Sagan increased his lead in the green jersey competition to 209 points, with Goss in second on 178 and Greipel third with 167. World champion Cavendish, pipped by Goss in the intermediate sprint earlier in the day, stays in fourth place after finishing a huge six minutes down on Sagan.
Race favourites Evans and Wiggins crossed the line in the main pack four seconds down on Sagan. Also safely arriving in Metz were Vincenzo Nibali (Liquigas), Denis Menchov (Katusha), Andreas Kloeden (RadioShack), Jurgen van den Broeck (Lotto Belisol), Sylvain Chavanel (Omega Pharma-Quick Step) and the yellow jersey, Cancellera.
The Swiss leads Wiggins and Chavanel by seven seconds in the GC, with Menchov 13 seconds down in fifth and Evans poised in sixth, at 17 seconds.
Stage six marked a grey day for the likes of GC riders Scarponi, Brajkovic, Schleck and Valverde, who crossed the line in a main chasing group that also included Jelle Vanendert (Lotto Belisol) and last year’s white jersey Pierre Rolland (Europcar), 2:09 down on Sagan.
Dutch hope Gesink, who had been involved in two earlier crashes as well as the large pile-up 25km from the finish, lost 3:31, while it was much worse for Garmin’s Hesjedal, who crossed the line bloodied and bruised a massive 13:24 in arrears before being taken to hospital for tests.
Four riders were forced to abandon the race, including another Garmin rider, the American Tom Danielson, who finished eighth in the 2011 Tour.
The race continues on Saturday with the 199km stage seven into the Vosges mountains, which finishes atop the first-category Planche Des Belles Filles climb.