The 32-year-old won the 197.2km stage between Tudela and Valdezcaray by 37 seconds over Alex Zulle, a victory that left him with a 33sec overall lead over his compatriot after starting the day trailing by four seconds.
The victory was Rominger's second following his win in Thursday's 11th stage. Known primarly as a sprint specialist, Rominger, who is attempting to become only the second rider to win the tour back-to-back, is proving to be invincible in the mountains.
Colombia's Oliverio Rincon finished third while Spain's Laudelino Cubino was fourth - both 43 seconds adrift.
Pedro Delgado, Spain's 33- year-old attempting to win the race for a record third time, is in seventh place overall, 6min 49sec behind Rominger and virtually out of contention in the 21-day event.Reuse content