De Gendt made a move to the front with more than 20km to go and held on until the end to clinch the 199km stage from Sant Cugat del Valles to Setcases.
“The headwind at the end of the stage was lethal, but I survived," De Gendt said. "The tactics of the GC riders were an advantage for me. Quintana, for example, stopped pulling in the chasing group. I only had to pedal hard.
"The closer I got to the finish, the more I wanted to win. The last twenty kilometres were very hard nonetheless. It was only in the last three kilometres that I started to believe that I could win. The road went uphill until one kilometre from the finish and there was that strong headwind.
"I knew that if someone would attack from the bunch it would soon be over for me because I had nothing left in the tank. The way I win is one of the greatest performances of my career.”
The Lotto Soudal breakaway specialist finished 20 seconds in front of the chasing peloton, earning a 23-second overall lead over Movistar's Valverde. Australia's Jay McCarthy is third overall at 27-seconds.
Stage 4 will take the peloton 170km from Llanars to Alp with the seven-stage race ending on Sunday in Barcelona.
“It will be difficult to maintain the leader’s jersey tomorrow, with a summit finish on La Molina," De Gendt said. "I only have a small lead.
"As a team, we have achieved our goal of winning a stage and we have a nice bonus. I will try to hang on as long as possible tomorrow, but I assume I will lose the jersey. Which wouldn’t be a disgrace considering the riders in this peloton.
"It will also be difficult to win the KOM jersey here because there are a lot of points to win tomorrow but as a leader, I won’t be allowed to join the breakaway. I’ll see the day after tomorrow what’s still possible in the KOM classification.”
