The Frenchman made it into the day's vital break to hunt the 40 maximum points on offer over the four category one climbs.
While Wout Poels (Ineos) captured the maximum points over the Puerto de Navacerrada as the breakaway took some time to establish into a cohesive group, Bouchard grabbed the next best six points. Poels' team mate Tao Geoghegan Hart happily conceded the next 10 on the Puerto de la Morcuera but Bouchard attacked the leaders some kilometres from the top of the second ascent of la Morcuera to secure his grip on the blue polka dots.
Higuita took the final maximum points but the damage was done. Bouchard's 32 point lead over Angel Madrazo all but securing him the KOM crown.
“I took as many points as I could today," Bouchard said. "We knew it would be hard to resist Astana in the finale so we had to score as much as possible before the favourites came back."
27-year-old Bouchard who joined AG2R as a trainee last season has not yet competed in or completed a grand tour.
"I’ve never done a third week of racing so I’m going without too much pressure," he said. "I can’t say if it will work or not. It’s very much a mental thing. You need to be fresh in the morning in the bus. It’s not always easy, but I want to ride my bike and I enjoy it. I’m super motivated for this kind of stages.
"The jersey is almost won. I managed to put some distance between me and my main rivals so it’s a good thing."
