The Kazakh team covered the 13.4 kilometre in 14 minutes 51 seconds to overhaul Deceuninck-Quick Step by two seconds and Sunweb by five.
The young Colombian climber will enjoy a Grand Tour leader’s jersey for the first time in his career as he sets his eyes on the overall podium in Madrid.
“I’m very happy because we’ve done things well. It’s been thanks to the whole team, to everyone’s effort, that we took this victory," Lopez said.
"We didn’t make a choice (as to who would cross the line first). It happened on the fly. I was second behind Gorka [Izagirre] when we entered the last curve and he let me pass so I would ride the last 150 metres."
The powerful Jumbo-Visma squad lost 40 seconds after riding through a nightmare first stage with Primoz Roglic and Steven Kruijswijk crashing hard, as well as a Sepp Kuss mechanical causing headaches for the high-flying Dutch squad.
UAE Team Emirates also had a horror start with Fabio Aru as all bar one crashed in a mass pile-up as a wet patch out on course caused by a burst paddling pool.