Both crashed separately on the final climb in the gravel section, vision of their plights not captured by the host broadcaster due to treacherous conditions.
Lopez was on the attack and looked set to put in at least 50 seconds into his rivals when he crashed down on the Alto Els Cortals d’Encamp.
"I felt really good and I attacked on that climb as we planned," he said. "Later, I’ve got a big help from Gorka and Jakob. I was pushing as hard as I could, and everything was OK until the moment I crashed down.
"It was very hard to handle the bike under that heavy rain on a gravel sector. Fortunately, I did not get any serious injury, but I lost time and my rivals came across me. I continued working hard, trying to stay in that group, but gravel and mud have damaged my bike, while there was no place to change it.
"I am still happy with my form and I realized I am good right now. Still two weeks in La Vuelta and we will keep on fighting,
The Colombian finished the stage 38 seconds behind Nairo Quintana and sits third overall, just 17 seconds behind his compatriot.
Roglic looms just six seconds behind the new race leader despite also falling on the gravel section, the team blaming a moto for the crash.
“It was very chaotic at one point," Jumbo Visma sports director Addy Engels said. "Not only because of the gravel, but also because of the bad weather conditions.
"Primoz crashed on the gravel due to a stationary motorbike. That is not okay and should not happen.
"All in all I think that, given the situation at one point, we have done some good business GC-wise. We are in a good position before Tuesday's time trial. Although we will never know what would have been possible without that crash.”
The Vuelta a Espana resumes on Tuesday night after a rest day, LIVE from 11pm AEST and nightly on SBS Viceland or catch up with the daily highlights on SBS at 5pm.