The 26-year-old Colombian is now the fourth most successful rider to race for the Spanish squad but is still well shy of Miguel Indurain's 97-win tally that was set in the 1990s.
Quintana, who is once again using the Route du Sud as his final build up race before the Tour de France, finished the final stage safely in the pack as another rider looking for form ahead of the Tour - Arnaud Demare (FDJ) - won ahead of Yohann Gene (Direct Energie) and Stéphane Poulhies (Armee de Terre). Movistar claimed second overall in the race, with Marc Soler finishing 36 seconds off Quintana's overall lead. The Spaniard also took the young rider's jersey.
"It's a very important victory. I was coming into this event following long weeks of training in altitude at home in Colombia, and I could confirm I'm in good form," Quintana said after wrapping up the overall win.
"Legs have gone as usual for me in the mountains and it seems obvious that I've improved quite a bit into the time trial," he added.
Quintana won the Route du Sud in 2012 and finished second last year to Alberto Contador. His form this annum is clearly on the rise. Despite a long break from racing after training in Colombia he is well on track to compete for the overall win in the Tour de France. He has been consistent throughout this season, too, winning the Tour of Catalunya and the Tour of Romandie in impressive fashion.
At the finish on Sunday he confirmed that his form was in a good place and that mentally he was ready for the Tour de France campaign.
"The team did really well: great job from them from the beginning to the end of the race, crowning it today after a mountain stage where they rode fantastically, including Marc's win. Both victories in the race – this overall win I confirmed today and my first success in 2012- have been really significant into my sporting career and for my preparations for the Tour. Reaching the 'Grande Boucle' this way feels really good."