Spaniard Valverde and his Movistar team-mate Eros Capecchi both crashed on an unclassified descent which race organisers had identified as a dangerous area with around 100km remaining on the mountain-dominated stage.
The team tweeted that the crash - which occurred away from the television cameras - "does not seem to be of serious consequences", referring to any injuries Valverde may have sustained.
The 217.7km stage four featured five categorised climbs and began in Camprodón, with an 18.9km HC mountaintop finish in Port Ainé.
Garmin-Sharp rider Martin soloed to a significant 36-second victory ahead of Katusha's Joaquim Rodriguez, who had assumed the virtual lead of the race from Valverde after the crash, and stage three winner Nairo Quintana.
Colombian Quintana will now be the focus of Movistar's assault on the GC. He stands 32s behind Martin, with Rodriguez 10s off the leader.
Tour de France champion Bradley Wiggins finished sixth, over a minute behind the winner, and is now fourth overall, 36s behind Martin.
Martin was part of a 25-man breakaway that formed an hour into the stage, and the sole rider to stay out in front.
Once the peloton had sucked the other 24 riders back in and the final climb begun, Jurgen van de Broeck (Lotto Belisol) and Robert Gesink (Blanco) attacked but were passed by Rodriguez and Quintana with less than a kilometre remaining. Van de Broeck finished alone in fourth, with Gesink four seconds back in fifth.
Wiggins led home Peter Stetina (Garmin-Sharp), Michele Scarponi (Lampre-Merida) and Thomas Danielson (Garmin-Sharp).
Valverde took the lead on Wednesday having finished six seconds behind Quintana in a three-man group containing 2010 Catalunya winner Rodriguez and Wiggins.
The seven-stage race, the first this year in which Briton Wiggins intends to fight for overall victory, ends in Barcelona on Sunday.