Speaking after the finish, Sagan has thanked his team for their "continued support" as his contract with Bora-Hansgrohe is in doubt for next season.
Sagan was perfectly placed going into the final few corners as he battled for Colbrelli's (Bahrain Victorious) wheel. His team relied mostly on the team of the overall leader Rohan Dennis (Ineos Grenadiers) to do most of the day's work before starting their chase with around 40km to go.
The former three-time world champion has not raced the Tour de Romandie since 2010 where he won ahead of Francesco Gavazzi (then Lampre-Farnese Vini) and Nicolas Roche (then Ag2r La Mondiale) in a bunch sprint to take his third ever career victory.
Speaking after the finish, Sagan said: "I'm really happy to win again in the Tour de Romandie. In 2010 I had taken the first road stage and here I am eleven years later with another victory.
"I have to thank my teammates for their great job today, in the last two laps they were pulling in the front and after the last climb, they held the bunch together.
"It feels nice after three weeks without any racing to come here and win, probably the only stage suited to me because the following ones will be very hard. Thanks as well to the whole team and its sponsors for their continuous support."
Last month, Bora-Hansgrohe team manager Ralph Denk raised doubts about Sagan's future with the team, questioning how long the three-time world champion can justify his salary with his performances on the road.
Sagan, who put in a very strong time in the prologue on the race's first day, has now moved up to fifth in the overall standings just twelve seconds behind Dennis and three seconds behind Geraint Thomas and Richie Porte (both Ineos Grenadiers) on the podium spots.
Team sports director, Jan Valach said: "It was a nice stage for us today but a hard one as well, with 2,600 metres of altitude gain. The goal we had set was to win, we all worked towards it and we achieved it.
"We controlled from the start to avoid having a big breakaway group, Juraj [Sagan], Jordi [Meeus], and Marcus Burghardt put in a big effort to keep things under control. Juraj and Jordi contributed to catching the break while Burgi placed the squad in the right position before the final climb.
"Then, Ben [Zwiehoff] was essential in bringing back all the late attacks in the closing, flat, kilometres. This excellent teamwork was finally capped off with a good sprint by Peter and a stage win.
"Last but certainly not least, Wilco [Kelderman] was always in the leading front group and finished safely with the main GC contenders."
Stage two suits a rider who can get over the hills but also have a fast finish. It could potentially be another perfect day for Sagan, but he comes up against some very solid riders like Marc Hirschi (UAE Team Emirates) and Alexey Lutsenko (Astana-Premier Tech).
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