Moreno moved away from the splintering pack late on the 2.4km climb to Saint-Felicien to claim his biggest victory since a mountain top stage win in the Vuelta a Espana last September.
France's Julien Simon took second place behind the Katusha rider on the fast-paced, sinuous 160 kms stage through the verdant Ardeche hills, with Frenchman Tony Gallopin finishing third.
"I attacked with 200 metres to go, and could stay away, it wasn't so complicated," Moreno told reporters. "I knew this kind of finish suited me, so even if other people didn't consider me the favourite, I did.
"Together with my victory in the Vuelta and the win in the Tour of Piamonte (in 2011), this is one of the three most important wins of my career."
Moreno's role is usually that of key wingman for Spanish stage race specialist and Katusha team mate Joaquim Rodriguez, recently runner-up in the Giro.
But with Rodríguez, a double Criterium du Dauphiné stage winner last year, making a late decision not to race, Moreno has had more freedom to strike out in his own right.
"It was a very difficult finish, everybody was getting nervous on the downhill before this little climb. But I knew I could have a chance here," he said.
Ninth on the stage, defending champion Wiggins remains the overall leader, with Australian Cadel Evans in second and Andrej Grivko of the Ukraine third.
Keen to repeat his victory on stage one, Evans' BMC squad kept the pace on the fast, sweeping descent that precedes the final climb.
First the Australian and then world time trial champion Tony Martin steadily upped the pace at the front of the pack on the last steady but shallow ascent, but Wiggins was more than able to handle the change of rhythm.
The race finishes in Chatel on Sunday.