Sagan (Bora-Hasngrohe) took the victory ahead of Fernando Gaviria (UAE Team Emirates) thanks to his team's efforts to get rid of several sprint rivals on a hilly section earlier in the day.
Egan Bernal (Ineos Grenadiers) retained his overall lead, crossing the line in the main pack. His lead over Remco Evenepoel (Deceuninck-QuickStep) has been reduced from 15 to 14 seconds.
Sagan capitalised on lead-out from Juan Sebastián Molano (UAE Team Emirates) in the last 400 metres, coming out of the final bend in front and successfully holding off the challenge of Gaviria, while Davide Cimolai (Israel Start-Up Nation) took third place further back.
The Slovakian had his team push hard on the unclassified Cantoniera and fourth-category climb of the Valico della Somma climbs around 40 kilometres from the finish of the race's shortest road stage.
They successfully neutralised Dylan Groenewegen (Jumbo-Visma), Giacomo Nizzolo (Qhubeka Assos), and Stage 2 winner Tim Merlier (Alpecin-Fenix), leaving only a handful of top sprinters to contend the finish.
Sagan's win – and the 50 points that came with it – means he now holds the maglia ciclamino as leader of the points classification, enjoying a 17-point lead over Gaviria and Cimolai.
"I think was a very good day for us," Sagan said after the race.
"We tried our best, and in the end, I won and I'm very happy for that. I have to say thanks to all my teammates.
"When Caleb Ewan won the second stage, I was very good. It was an uphill and I had very good legs. I started from a little back and I had good speed, but I was closed on the barriers and luckily, I didn't crash.
"Today I'm very happy to win a stage like this. It was a great effort from all the team. Day by day – we still have halfway to go and I will try my best [for the points jersey]."
