Bilbao attacked the descent inside the last three kilometres to finish ahead of team-mate Luis Leon Sanchez and Ivan Ramiro Sosa (Androni-Sidermec-Bottecchia).
He was part of the leading group which was formed on the final slopes of the last climb of the day and with five Astana riders represented in the lead group, Bilbao capitalised on his strength in numbers to attack and take a narrow lead through to the finish.
"We were motivated to do something good today, and in the final, we had a very good situation with five riders of our team in the leading group," Bilbao said. "It was a perfect position to try. The last kilometres of the climb was quite difficult with several attacks and a small gap between the riders on the top. But, later we could return in front.
"On the descent, I saw my chance and I made an attack, immediately getting a small gap. Yeah, I was not sure at all I could do it until the end, knowing about the final uphill of 500 meters.
"Anyway, I was able to recover a bit on the final short descent and did my best inside the last kilometre. I am so happy with this victory, I’ve been waiting for it for a long time. Also, I am happy with all our team, we did a very strong and smart stage.
Bilbao will take the race lead into the most difficult in the five-stage race, with 145km of road between the start at Lavarone and finish on l'Alpe di Pampeago.