The Liquigas all-rounder was untouchable in the climax to a chaotic 197km stage through north France, beating Norway's Edvald Boasson Hagen (Team Sky) by a few bike lengths after a typically explosive finish.
Race leader Fabian Cancellara (RadioShack) retained his yellow jersey after finishing strongly in fourth place - but there was a blow for Bradley Wiggins, who lost Sky team-mate Kanstantin Siutsou after the Belorussian withdrew from the race with a broken tibia.
Wiggins is still trails Cancellara by seven seconds in the GC, with France's Sylvain Chavanel tied for time in third.
It was Chavanel who led a decimated peloton on to the last of six minor climbs in an incident-strewn stage after an audacious solo attack 5km from the finish.
But the Omega Pharma-Quick Step rider did not have the legs to hold the chasing riders at bay, his slender 10-second lead vanishing as soon as the final sprint commenced inside the closing 500 metres.
Defending champion Cadel Evans (BMC) and the in-form Swiss Michael Albasini (Orica-GreenEdge) were two of a cluster of riders who took the fight to Sagan – but the 22-year-old Slovak showed just why he is cycling’s hottest property with a brutal display to double his tally in his first ever Tour de France.
With the peloton split after a big crash just 200m from the line, Sagan pulled out a huge gap. The green jersey looked over his shoulder and had time to perform another zany celebration – this time, the Running Man – before securing the win.
Boasson Hagen took second place ahead of Peter Velits (Omega Pharma-Quick Step) and Cancellara, with Albasini pipping Evans for fifth.
Wiggins was held up by the final crash and crossed the line 47 seconds behind but received the same time at the finish as his main rivals because the incident occurred during the final 3km.
The British co-favourite will be knocked by the withdrawal of his team-mate Siutsou, who was forced out of the race after breaking a leg in one of the numerous pile-ups that marred an intriguing day of racing.
Also withdrawing during a chaotic stage four was Spaniard Jose Rojas (Movistar), who broke a collarbone in another crash inside the final 30km.
A combination of frequent crashes, numerous punctures and narrow, winding roads meant many riders lost contact with the main peloton during the stage. Those hit badly were included last year’s yellow jersey hero Thomas Voeckler (Europcar) and Belgian Philippe Gilbert (BMC), who both lost more than seven minutes.
Vuelta runner-up Chris Froome (Team Sky) and Russian veteran Denis Menchov (Katusha) were also held up - but like Wiggins, they were awarded the same time as the chasing group behind Sagan.
Luck was not so generous to Garmin-Sharp, for whom Christian Vandevelde lost 2:08, Dan Martin 5:05 and Tom Danielson a huge 9:11. Giro d'Italia Ryder Hesjedal has been involved in at least two crashes - but the Canadian managed to finish safely in the main group.
Played out under ominous grey skies and the odd patch of drizzle, stage four was animated early on by a break of five riders, including the polka dot jersey Michael Morkov (Saxo Bank-Tinkoff Bank).
Attacking for the third day in succession, Morkov and his fellow escapees - Ruben Perez (Euskaltel), Giovanni Bernaudeau (Europcar), Sebastien Minard (Ag2r-La Mondiale) and Andriy Grivko (Astana) - built up a lead of seven minutes over a largely flat first two thirds of racing.
Morkov picked up maximum points over the first four minor climbs of the day to consolidate his lead in the king of the mountains competition.
Ukrainian national champion Grivko was the last of the initial five leaders to be caught by the main chasing group, the Astana rouleur being swallowed up on the penultimate climb of the day inside the final 10km.
By this point, the race had been blown apart by many crashes and the testing terrain. Stage two winner Mark Cavendish had picked up maximum points for sixth place at the intermediate sprint, but the world champion was one of many riders distanced by the leaders in a tempestuous lead in.
Sagan’s victory was his 15th of the season and the Slovak became the first rider since Tom Boonen in 2004 to pick up multiple stage wins in a debut Tour.
Sagan also extended his lead in the green jersey competition, in which he now holds 116 points to Cancellara’s 74. Cavendish is currently third, on 73.
The race continues on Wednesday with a long 214.5km stage from Abbeville to Rouen, which features four lower category climbs and hugs the Normandy coastline for a significant stretch.