Valverde and his Movistar team-mates were belatedly penalised by race officials, with BMC Racing awarded victory in the team test against the clock and Ben Hermans inheriting the race lead from Valverde.
The Spaniard responded by winning stage three, accelerating away from Ireland's Dan Martin (QuickStep Floors) to win the 188.3-kilometres mountainous route from Mataro to La Molina.
Adam Yates (Orica-Scott) was third, three seconds behind, alongside fellow Briton Geraint Thomas (Team Sky), who was sixth.
American Tejay van Garderen (BMC Racing) was eighth, also three seconds behind Valverde, to take the overall lead.
Van Garderen leads by 41 seconds from BMC Racing team-mate Samuel Sanchez, with Thomas three seconds further adrift and Valverde fourth, 44 seconds behind. Three-time Tour de France winner Chris Froome is fifth, 49secs back.
The day's racing was overshadowed by the ongoing recriminations from Tuesday's team time-trial.
Television pictures showed Movistar's Nelson Oliveira touching the lower back of team-mate Jose Rojas - who was in line to take the overall lead in the race - during the stage, prompting other teams to complain.
Rules state that under such circumstances each member of the team should have one minute added to their time.
But initially commissaires chose to add a minute to Oliveira's time and three to Rojas' time, while keeping Movistar as winners of the stage.
BMC finished two seconds behind Movistar, whose eight riders were given a one-minute penalty on Wednesday morning.
Movistar said in a statement on Wednesday afternoon: "The Movistar team wants to express its complete disagreement towards the sanction received.
"It's a penalty due to an infringement which we consider absolutely non-existent.
"The rider performing the action does not 'push' his team-mates, but touches the back of them with his right hand to warn them that they must take his position into the team row, a fact that doesn't influence the race's outcome at all."
Movistar suggested the demotion "sets a dangerous precedent".
Thursday's stage four is the 194km route from Llivia to Igualada.
