The Lotto Soudal rider took the maximum points on offer for each of the first five climbs, a total of 17, to amass a category-leading 74 and putting him 10 ahead of former classification leader Luis Ángel Maté (Astana). Bauke Mollema (Trek-Segafredo) is third on 60 points.
"Mission accomplished today and I am very happy with that," De Gendt said. "At the start of the stage, I remained at the back of the bunch to make sure I wouldn’t waste any energy by joining any moves on the first flat kilometres.
"As we were approaching the top of the first climb, I moved up towards the front of the pack. I crossed the top first and soon after the break was established.
"There were many strong riders in our group and I knew this was the break of the day. We immediately cooperated well and from then on it was my goal to get first to the top of the next climbs, that’s why I tried to save some energy at first.”
De Gendt, who finished 34th on the stage, five minutes and 26 seconds behind breakaway companion and eventual stage winner Michael Woods (EF Education First-Drapac), is now prepared for a final showdown on Stage 20, a short and mountainous 97.3km in Andorra.
The stage contains three Cat-1 climbs, a Cat 2 and Cat-3 with a combined 4000 metres of elevation over the short distance and a finish on the Coll de la Gallina, Andorra's most difficult ascent.
"Now it’s all about defending my jersey on Saturday," he said. "That will be the most important day in the battle for the KOM jersey. I now have some advantage over my opponents and that’s always good of course.
I think Mollema and [Ben] King Dimension Data) will be my most dangerous opponents. Maté, who’s now second in the KOM classification, has been ill for a few days now. Maybe he can recover the next two days and take part in the battle on Saturday.
"It would be great if the four of us would all be in the break and we have to sprint for the points on each climb.”