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Belgian Jasper Stuyven had spent almost the entire 183km stage from Saint-Lo to Cherbourg in the lead but was agonisingly caught in the final kilometre.
Frenchman Julian Alaphilippe took second with Spain’s Alejandro Valverde third.
On Monday, Sagan will wear yellow for the first time, but coming up the final hill, he had no idea he was riding for a stage win.
“I’m very surprised I won. I thought there were still two guys in front,” admitted the 26-year-old.
“Only at the very end I realised we were sprinting for victory. I’m very happy to be first.”
It continued a stunning last 12 months for Sagan, who won the world title in September before claiming his first ‘Monument’ one-day classic at the Tour of Flanders in April.
“Julian Alaphilippe was very close to me at the end but I beat him,” added Sagan.
“I’m in yellow first time. It’s a very nice jersey. This is something special for sure.”
Alaphilippe said he launched his sprint too soon.
“I saw the 400m to go sign, then 350m. It seemed to me that Sagan’s speed was stagnating, but no! I think I went too soon,” said the 24-year-old, who will wear the top young rider’s white jersey on Monday.
“He (Sagan) has a lot of talent, he’s world champion.
“I’m a bit disappointed today but it’s still good to be on the podium (to collect the white jersey).”
Contador crashed again
Reigning champion Chris Froome came home safely in 10th while Nairo Quintana was 17th, but one of their main overall rivals, Alberto Contador lost 48sec after crashing for the second day in a row.
The 33-year-old Spaniard who won the Tour de France in 2007 and 2009 injured his right side in Saturday’s crash and fell on it again early in Sunday’s stage.
When the race reached its tough uphill finale, Contador simply couldn’t keep pace.
But things were even worse for Australian Richie Porte, another with overall aspirations, who punctured in the last 5km and lost a 1min 45sec.
The finale was tough and 2014 champion Vincenzo Nibali as well as top French hope Thibaut Pinot both lost 11sec.
For Sagan it was his fifth Tour stage victory but first since 2013.
His sprint finish was too strong for Alaphilippe, who had gone past Sagan around 300 metres from home but then could not hold on as the Slovak came storming back past him.
The heartbreak was worse for Stuyven, who had attacked alongside German Paul Voss, Norway’s Vegard Breen and Cesare Benedetti of Italy right from the start of the stage.
The former world junior champion ditched his breakaway companions 8.5km from the end of the race on a short climb but after more than 182km in front, the Belgian 24-year-old tired badly towards the end and was gobbled up by a charging peloton.
The four-man breakaway had looked set to go all the way at one point as the peloton laboured in launching its chase.
They opened up a 5min 30sec advantage after just 20km and took that up to almost 7min at one point.
They still had 5min as the race entered the final 40km and Stuyven was a couple of minutes ahead with 12km left, which wasn’t enough.
Once the chase began, with Sagan’s Tinkoff team and the BMC squad of Belgian Greg Van Avermaet coming to the fore, the pace became relentless, with dozens of riders straggling out the back long before the pack reached the tough final 3km.
In winning, Sagan relieved Briton’s Mark Cavendish, who won Saturday’s opening stage, not only of the yellow jersey but also the green points jersey.
Stuyven’s only consolation was taking possession of the polkadot king of the mountains jersey off breakaway companion Voss.
Alaphilippe is now second overall to Sagan at 8sec with Valverde third at 10sec.
Froome is fifth at 14sec, two places ahead of Quintana, who is on the same time.
Contador is now down in 62nd at 1min 02sec, while Porte is 81st at 1:59.