The pocket climber of the Movistar team was left behind several times in the final climb by Pinot (Groupama-FDJ) and the Ecuadorian Jefferson Cepeda (EF Education) but he was the smartest at the finish to take the best victory of his career.
He won with six seconds ahead of Pinot and 1 min 35 sec on the main favorites who neutralized themselves in this 13th stage long of only 74 km.
The organizers had decided to plane the course by removing the Col du Grand-Saint-Bernard because of bad weather and the general state of disrepair of the peloton.
Britain's Geraint Thomas retained the leader's pink jersey, two seconds ahead of Slovenia's Primoz Roglic.
Thibaut Pinot took back the blue jersey of best climber and joined the Top 10, in tenth place, 3:13 from the pink jersey.
But it is a small consolation for the climber from Franche-Comté who dreams of winning a second stage in the Giro, after the one in 2017 in Asiago, before retiring at the end of the year.
The 32-year-old Frenchman was the big host of the day but perhaps wasted too much strength arguing non-stop with one of his breakaway companions, Cepeda.
The two men appeared to be the strongest, but kept attacking each other and then shouting at each other, while behind Rubio remained focused on his effort, without flinching.
"It's a great day for me, I worked a lot for this result. Pinot and Cepeda were very strong, I knew I had to keep them in my sights," said the Colombian who took the lead from the first pass of the day, the Croix-de-Coeur, also accompanied by Derek Gee and Valentin Paret-Peintre.
After a piece of valley together, the trio Rubio-Pinot-Cepeda broke away in the final ascent to Crans Montana to engage in a fierce and electric fight.
Very disappointed at the crossing of the line, Thibaut Pinot, sick last week, however finds the form at the right time, before a third week particularly mountainous.
© 2023 AFP