Second behind Sagan in the sprint of around 30 riders that decided the 167-km eighth stage from Tubach was Australia's Matt Goss, with Britain's Ben Swift third.
The leading group of some 30 riders, including race leader Cunego, sheered off the front of the pack on a third-category climb with around 25 kms to go.
After a frantic last 25km in which several top sprinters, including Britain's Mark Cavendish, were left behind by a split in the peloton a powerful sprint to the finish by the Slovakian's left Australian Matt Goss in second with Britain's Ben Swift in third place.
"It was a really hard finale but thankfully in the final kilometer I had (teammate) Daniel Oss leading me out," said Sagan, who also secured the race's blue jersey for the points competition.
"I'm very satisfied with this second win and the points jersey. It's been a huge success for me this week." Lampre rider Cunego meanwhile retained the race leader's yellow jersey with a 1min 36sec lead on Dutchman Steven Kruijswijk ahead of the race-closing time trial here on Sunday.
Cunego had stayed at the front of the main chasing peloton as it pursued an earlier breakaway, an intelligent move given what was to happen in the final, hilly kilometers.
After Cavendish's team had spent energy driving the chasing peloton, the American outfit were outfoxed when Movistar upped the pace on the category three Hallauerberg climb whose summit was 22km from the finish.
"We wanted to try and eliminate as many sprinters as possible" explained the Spanish team's sporting director Jose Luis Arrieta, whose main hope Jose Joaquin Rojas would eventually finished sixth.
The Garmin team of Norwegian sprinter Thor Hushovd soon joined in, and the Leopard team put German powerhouse Jens Voigt on the front to do further damage.
Despite Goss making the cut for HTC-Highroad, their efforts ultimately left Cavendish and overall contender Mollema - second overall at 1:23 overnight - fighting a vain battle to close the gap.
It also pushed Leopard's defending champion Frank Schleck up to third place, still 1:41 behind Cunego, however emotions ran high at the finish line where it transpired that Mollema had suffered a puncture 15km from home.
Mollema, who dropped to fifth overall at 2:11, accused Leopard of double standards and said their tactics will not be forgotten at next month's Tour de France.
"It's unbelievable they (Leopard) hit full gas when they heard I wasn't in the group any more," said the Dutchman.
"Last year in the Tour de France the Leopard guys (then riding for Saxo Bank) neutralized the race when some of their guys had crashed.
"We won't forget this when it comes to the Tour de France." American Levi Leipheimer of RadioShack is still 1:59 behind the Italian race leader, and the biggest threat on Sunday when a hilly 32.1 km race against the clock will decide the race.
Cunego, however, remained defiant.
"I've got quite a good lead and I'm in great form at the moment so it's up to the guys behind me to catch me," said the Italian.
Schleck's younger brother Andy, who has shown mixed form this week as he primes his condition for an assault on the Tour de France yellow jersey, secured the king of the mountains' green jersey.
Frenchman Lloyd Mondory of AG2R secured the blue jersey for the sprint competition.
The race finishes on Sunday with a 32.5-km individual time trial in Schaffhouse.
