Sagan, a 20-year-old former mountain bike specialist, won two stages of the Paris-Nice race in March and he outpaced the field again on the 175.6 kms from Porrentruy to Fleurier - a bumpy stage that proved too demanding for Briton Mark Cavendish.
Running second after Tuesday's prologue, Sagan proved he was also at ease in bunch finishes when he outshone Italian sprinter Francesco Gavazzi and Nicolas Roche, the son of former Tour de France champion Stephen.
"I didn't feel too well on the first two climbs of the day but much better on the third," said Sagan, an all-rounder who might be pretty hard to dislodge from the overall lead.
When Cavendish started to drift back on the roads of the Val de Travers, home of the fearsome Absinthe spirit, Sagan's Liquigas team mates, including former Giro winner Ivan Basso and title-holder Roman Kreuziger, set a quick pace to leave the Briton as far back as possible and he eventually crossed the line over nine minutes behind the winner.
