Top seed Nadal's straight-sets win over his compatriot sets up a semi-final meeting with Frenchman Jeremy Chardy, who later defeated Italy's Paolo Lorenzi in straight sets, 6-2 6-3.
The other semi will be an all-Argentina affair after Carlos Berlocq took a walk-over in his quarter final against Guillaume Rufin, while Horacio Zeballos saw off Albert Ramos 6-1 5-7 7-6 with a deciding-set tie-break victory.
Nadal broke Gimeno-Traver three times and wiped away four break points against his serve in the final game of the match to wrap up the quarter-final victory in 84 minutes.
"Today I had more confidence than the other days," said Nadal. "That is positive. It gives me confidence, and reasons to believe that I'm on the right way.
"I'm happy to win in singles against a tough opponent like Dani and to reach the semi-finals after seven months.
"In this tournament I had a good feeling. The crowd gave me their support all the time. It helps a lot when you come with a bad feeling."
The 11-time Grand Slam champion is looking to clinch the title on his season debut, having been sidelined for seven months with a left knee injury.
ATP Vina del Mar results
1-Rafa Nadal (Spain) beat 7-Daniel Gimeno-Traver (Spain) 6-1 6-4
3-Jeremy Chardy (France) beat 6-Paolo Lorenzi (Italy) 6-2 6-3
Horacio Zeballos (Argentina) beat 5-Albert Ramos (Spain) 6-1 5-7 7-6(6)
8-Carlos Berlocq (Argentina) beat Guillaume Rufin (France) WO